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| | | |
| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
− | == Tuesday - Start INDEL Calling == | + | == Tuesday - Start SNP Calling == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | === Setup === | + | === Setup Screen === |
− | The indel & snpcall pipelines will run overnight, but you'll want to log out. | + | The snpcall pipeline will run overnight, but you'll want to log out. |
| ; How do I leave something running on the server even if I log out? | | ; How do I leave something running on the server even if I log out? |
| : One solution is screen! | | : One solution is screen! |
Line 24: |
Line 24: |
| * It should now look basically the same as your normal command line. | | * It should now look basically the same as your normal command line. |
| | | |
| + | === Setup Variables === |
| Set these values. Also, be sure to specify your sample name instead of SampleXX | | Set these values. Also, be sure to specify your sample name instead of SampleXX |
| export SAMPLE=SampleXX | | export SAMPLE=SampleXX |
− | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt | + | or |
| + | export SAMPLE=NA12878 |
| | | |
− | See the settings you just used:
| + | Point to your GotCloud & your output directory: |
− | cat /net/seqshop-server/home/mktrost/seqshop/setupSS.txt | + | export GC=~/seqshop/gotcloud |
− | Shows you:
| + | export OUT=~/$SAMPLE/output |
− | :<code>export GC=/net/seqshop-server/home/mktrost/seqshop/gotcloud</code>
| |
− | :<code>export SS=/net/seqshop-server/home/mktrost/seqshop/singleSample</code>
| |
− | :<code>export OUT=~/$SAMPLE/output</code>
| |
| | | |
| === List of BAMs === | | === List of BAMs === |
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| * Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path). | | * Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path). |
| | | |
− | === Configuring Indel === | + | === Configuring SNPCALL === |
− | No special Configuration settings for Indel calling
| + | |
| cat ~/$SAMPLE/gotcloud.conf | | cat ~/$SAMPLE/gotcloud.conf |
| | | |
− | You will see something like this: | + | You will see this: |
| <pre> | | <pre> |
− | # Cluster Settings | + | # References |
− | BATCH_TYPE =
| + | SS_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample |
− | BATCH_OPTS =
| + | REF_DIR = $(SS_DIR)/ref/gotcloud.ref/ |
− | | |
− | OUT_DIR = Sample13/output
| |
| | | |
− | # Align Settings | + | ######### ALIGNMENT ######## |
| MAP_TYPE = BWA_MEM | | MAP_TYPE = BWA_MEM |
− | BWA_THREADS = -t 24
| |
| FASTQ_LIST = fastq.list | | FASTQ_LIST = fastq.list |
| + | BATCH_TYPE = |
| + | BATCH_OPTS = |
| + | BWA_THREADS = -t 6 |
| | | |
| # SNP Call Settings | | # SNP Call Settings |
| UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb | | UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb |
− | VCF_EXTRACT = /net/seqshop-server/home/mktrost/seqshop/singleSample/snpOnly.vcf.gz | + | VCF_EXTRACT = $(SS_DIR)/snpOnly.vcf.gz |
| MODEL_GLFSINGLE = TRUE | | MODEL_GLFSINGLE = TRUE |
| MODEL_SKIP_DISCOVER = FALSE | | MODEL_SKIP_DISCOVER = FALSE |
| MODEL_AF_PRIOR = TRUE | | MODEL_AF_PRIOR = TRUE |
| | | |
− | EXT_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample/ext | + | EXT_DIR = $(SS_DIR)/ext |
| EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz | | EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz |
| </pre> | | </pre> |
| | | |
− | === Running Indel Calling === | + | === Running SNP Calling === |
− | Run GotCloud indel with 6 jobs running in parallel | + | Run GotCloud snpcall with 8 jobs running in parallel |
− | * Why 6? | + | * Why 8? |
| ** You want to run as many as you can. | | ** You want to run as many as you can. |
− | ** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine | + | ** 2-3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine |
− | ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 | + | ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 8 --outdir $OUT |
− | * Only need the configuration & number of threads, rest is specified within the configuration. | + | * Only need the configuration, number of threads, and the output directory, rest is specified within the configuration. |
| | | |
| This will run overnight. We will check if it completed at the practical in the morning. | | This will run overnight. We will check if it completed at the practical in the morning. |
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| | | |
| exit PuTTY | | exit PuTTY |
| + | |
| + | |
| + | === FEEDBACK! === |
| + | Please provide feedback on today: |
| + | |
| + | https://docs.google.com/forms/d/1ADTkBjzT-QNj2lrejyqGqDaahTponrw20kSgDNwqwH4/viewform |
| | | |
| </div> | | </div> |
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| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| | | |
− | == Wednesday == | + | == Thursday == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| | | |
− | <div class="mw-collapsible" style="width:500px">
| + | === Checking if snpcall Completed === |
− | === Checking if INDEL Completed === | + | ==== Resume screen to Check Jobs ==== |
− | <div class="mw-collapsible-content">
| |
− | ==== Logging Back in to Check Jobs ==== | |
| | | |
| ;How do you log back into screen? | | ;How do you log back into screen? |
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| This will resume an already running screen. | | This will resume an already running screen. |
| | | |
− | Verify you got a "completed successfully" message.
| + | Your screen session still has your environment variables set, so you do not need to reset them. |
| | | |
− | How long did INDEL calling take? Look at the log message - time in seconds.
| |
| | | |
− | === Need a BAM Index File? ===
| + | Verify you got a "completed successfully" message. |
− | Check your BAM files
| |
− | ls $SAMPLE/output/bams/*bam
| |
| | | |
− | Check your BAI files
| + | How long did snpcall calling take? Look at the log message - time in seconds. |
− | ls $SAMPLE/output/bams/*bai | |
| | | |
− | Do you have the same number of BAM & BAI files?
| |
− | * If so, then you are good to go.
| |
− | * If you have more BAI's than BAM's - oops!!! (LET ME KNOW)
| |
− | * If you have more BAM's than BAI's, we need to generate the index:
| |
− | *: <pre>$GC/bin/samtools index $SAMPLE/output/bams/YOUR_BAM_WITH_MISSING_BAI.bam</pre>
| |
− |
| |
− |
| |
− | === Detach From screen===
| |
− | Detach from screen. We will resume it again later when we start SNPCall.
| |
− | Ctrl-a d
| |
− |
| |
− | </div>
| |
− | </div>
| |
− |
| |
− | === Structural Variation Tutorial ===
| |
− | Now we are going to run the Structural Variation Practical
| |
− |
| |
− | Please go to: [[SeqShop: Analysis of Structural Variation Practical, May 2015]]
| |
− |
| |
− | We will Start SNP Calling after the practical.
| |
− |
| |
− |
| |
− | <div class="mw-collapsible" style="width:500px">
| |
− |
| |
− | === Start SNP Calling ===
| |
− | <div class="mw-collapsible-content">
| |
− | ==== Resume screen ====
| |
− |
| |
− | ;How do you log back into screen?
| |
− | screen -r
| |
− | This will resume an already running screen.
| |
− |
| |
− | Your screen session still has your environment variables set, so you do not need to reset them.
| |
| | | |
| ==== List of BAMs ==== | | ==== List of BAMs ==== |
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| * Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path). | | * Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path). |
| | | |
− | ==== GotCloud SnpCall Configuration ==== | + | |
| + | ==== GotCloud INDEL Configuration ==== |
| | | |
| cat ~/$SAMPLE/gotcloud.conf | | cat ~/$SAMPLE/gotcloud.conf |
| | | |
− | You will see something like this:
| + | Same as it looked the other day with no special Configuration settings for INDEL calling. |
− | <pre>
| |
− | # Cluster Settings
| |
− | BATCH_TYPE =
| |
− | BATCH_OPTS =
| |
− | | |
− | OUT_DIR = Sample13/output
| |
| | | |
− | # Align Settings
| + | ==== Running INDEL ==== |
− | MAP_TYPE = BWA_MEM
| + | Run GotCloud indel with 6 jobs running in parallel |
− | BWA_THREADS = -t 24
| + | ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 --outdir $OUT |
− | FASTQ_LIST = fastq.list
| + | * Only need the configuration, number of threads, and the output directory, rest is specified within the configuration. |
− | | |
− | # SNP Call Settings
| |
− | UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb
| |
− | VCF_EXTRACT = /net/seqshop-server/home/mktrost/seqshop/singleSample/snpOnly.vcf.gz
| |
− | MODEL_GLFSINGLE = TRUE
| |
− | MODEL_SKIP_DISCOVER = FALSE
| |
− | MODEL_AF_PRIOR = TRUE
| |
− | | |
− | EXT_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample/ext
| |
− | EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz
| |
− | </pre>
| |
− | | |
− | ===== Configuration Updates =====
| |
− | '''No configuration updates from the original settings are necessary.'''
| |
− | * Originally you were going to update the configuration to do exome calling only, but we have decided to do whole genome
| |
− | ** If it doesn't finish tonight, we will kill it at the tutorial in the morning, and take advantage of the GotCloud restart capability after the tutorial tomorrow.
| |
− | | |
− | If you started making updates to your configuration yesterday, you can try to make it match above (mktrost is actually the path you want in the paths above).
| |
− | * The only difference from above should be your OUT_DIR.
| |
− | Check it with (leave as ~mktrost - you are comparing to my NA12878 conf file):
| |
− | diff $SAMPLE/gotcloud.conf ~mktrost/NA12878/gotcloud.conf
| |
− | | |
− | '''If you see differences other than OUT_DIR, you can modify your file using nedit (or your favorite editor as you used yesterday).'''
| |
− | * '''Or you can copy my file and just change OUT_DIR:'''
| |
− | cp ~mktrost/NA12878/gotcloud.conf $SAMPLE/gotcloud.conf
| |
− | nedit $SAMPLE/gotcloud.conf&
| |
− | * Edit OUT_DIR
| |
− | OUT_DIR = Sample##/output
| |
− | * Save, and close
| |
− | | |
− | ==== Running SnpCall ==== | |
− | Run GotCloud snpcall with 6 jobs running in parallel | |
− | * Why 6?
| |
− | ** You want to run as many as you can.
| |
− | ** 5 of you on the machine - 5*6 = 30 jobs will be running in parallel on that machine
| |
− | ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6 | |
− | * Only need the configuration & number of threads, rest is specified within the configuration. | |
| | | |
| This will run overnight. We will check if it completed at the practical in the morning. | | This will run overnight. We will check if it completed at the practical in the morning. |
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| exit PuTTY | | exit PuTTY |
| | | |
| + | === FEEDBACK!=== |
| + | Please provide feedback for today. |
| + | https://docs.google.com/a/umich.edu/forms/d/1iES6usHxLB7Ec9hRxtqYgH7v05lU3Ume4VJcksx8Ogg/viewform |
| | | |
| </div> | | </div> |
| </div> | | </div> |
− | </div>
| |
− | </div>
| |
− |
| |
− | <div class="mw-collapsible mw-collapsed" style="width:500px">
| |
− |
| |
− | == Thursday ==
| |
− | <div class="mw-collapsible-content">
| |
− | === Checking if SnpCall Completed ===
| |
− | ==== Logging Back in to Check Jobs ====
| |
− |
| |
− | ;How do you log back into screen?
| |
− | screen -r
| |
− | This will resume an already running screen.
| |
− |
| |
− | ==== Checking Completion ====
| |
− |
| |
− | Did you get a "completed successfully" message?
| |
− |
| |
− | If yes, how long did SNP calling take? Look at the log message - time in seconds.
| |
− |
| |
− | If no, are you running on seqshop-server? If so, KILL it. ssh -X to one of the seqshop machines and run on there.
| |
− | Ctrl-c
| |
− |
| |
− | Detach from screen. We will resume it again later when we restart SNPCall (if necessary).
| |
− | Ctrl-a d
| |
− |
| |
− | === Ancestry Tutorial ===
| |
− | Now we are going to run the Structural Variation Practical
| |
− |
| |
− | Please go to: [[SeqShop: Estimates of Genetic Ancestry Practical, December 2014]]
| |
− |
| |
− | We will Resume SNP Calling (if necessary) after the practical.
| |
− |
| |
− |
| |
− | === Restart SnpCall ===
| |
− | ==== Resume screen ====
| |
− |
| |
− | ;How do you log back into screen?
| |
− | screen -r
| |
− | This will resume an already running screen.
| |
− |
| |
− | Your screen session still has your environment variables set, so you do not need to reset them.
| |
− |
| |
− | ==== Running SnpCall ====
| |
− | Run GotCloud snpcall with 6 jobs running in parallel
| |
− | ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
| |
− | * GotCloud will pick up after the last completed step from before.
| |
− |
| |
− | This will run overnight. We will check if it completed at the practical in the morning.
| |
− |
| |
− | ==== Log Out ====
| |
− | ;Want to log out and leave your job running?
| |
− | In the screen window, type:
| |
− | Ctrl-a d
| |
− | (Hold down Ctrl and type 'a', let go of both and type 'd')
| |
− | * This will "detach" from your screen session while your alignment continues to run.
| |
− |
| |
− | exit PuTTY
| |
− |
| |
− |
| |
| </div> | | </div> |
| </div> | | </div> |
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| | | |
| | | |
− | === SeqShop: Ancestry On Your Own Genome, December 2014 === | + | === SeqShop: Ancestry On Your Own Genome, May 2015 === |
− | [[SeqShop: Ancestry On Your Own Genome, December 2014]] | + | [[SeqShop: Ancestry On Your Own Genome, May 2015]] |
| | | |
| + | === Setup Variables === |
| + | Set these values. Also, be sure to specify your sample name instead of SampleXX |
| + | export SAMPLE=SampleXX |
| + | or |
| + | export SAMPLE=NA12878 |
| | | |
− | === Association Analysis Tutorial ===
| + | Point to your GotCloud & your output directory: |
− | Now we are going to run the Association Analysis Practical
| + | export GC=~/seqshop/gotcloud |
− | | + | export OUT=~/$SAMPLE/output |
− | Please go to: [[SeqShop: Genetic Association Analysis Practical, December 2014]]
| |
− | | |
− | We will look at our own genomes again after the practical.
| |
− | | |
− | | |
− | === Return to SeqShop: Ancestry On Your Own Genome, December 2014 ===
| |
− | Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_December_2014#Checking_if_Pileup_finished]]
| |
| | | |
| === Reviewing Indel Results === | | === Reviewing Indel Results === |
− | Set these values. Also, be sure to specify your sample name (or NA12878) instead of SampleXX
| |
− | export SAMPLE=SampleXX
| |
− | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
| |
− |
| |
| Look in the output directory | | Look in the output directory |
| ls ~/$SAMPLE/output | | ls ~/$SAMPLE/output |
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Line 247: |
| The insertion deletion ratio increases from 0.91 to 0.92. | | The insertion deletion ratio increases from 0.91 to 0.92. |
| | | |
| + | === Return to SeqShop: Ancestry On Your Own Genome, May 2015 === |
| + | Return to [[SeqShop:_Ancestry_On_Your_Own_Genome,_May_2015#Checking_if_Pileup_finished]] |
| | | |
| === Friday: Reviewing SNPCALL Results === | | === Friday: Reviewing SNPCALL Results === |
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| | | |
| === Friday : More SNP Analysis === | | === Friday : More SNP Analysis === |
| + | In addition, set another environmental variable for locating the binaries for custom analysis |
| | | |
− | ==== Environmental Variables ==== | + | export HK=/net/seqshop-server/home/hmkang/apigenome/bin |
− | | + | export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/ |
− | If you didn't set the environmental variable, you can set it again
| + | export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref |
− | | + | export GC=~/seqshop/gotcloud |
− | source /net/seqshop-server/home/mktrost/seqshop/setup.txt | |
− | export SAMPLE=SampleXX (MAKE SURE TO CHANGE XX to your number or use NA12878 instead) | |
− | source /net/seqshop-server/home/mktrost/seqshop/setupSS.txt
| |
| | | |
− | In addition, set another environmental variable for locating the binaries for custom analysis
| |
| | | |
− | export HK=/net/seqshop-server/home/hmkang/seqshop/bin | + | export SAMPLE=SampleXX |
| + | export OUT=~/$SAMPLE/output |
| | | |
| ==== Annotation / Lookup against dbSNP ==== | | ==== Annotation / Lookup against dbSNP ==== |
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| If you want to add rsIDs to your variant files, you can do this by running the following command | | If you want to add rsIDs to your variant files, you can do this by running the following command |
| | | |
− | $HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz | + | $HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbsnp_142.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz |
| | | |
| If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs | | If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs |
| | | |
− | $HK/run-command-wgs --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6 | + | $HK/run-make --repeat-chr --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbsnp_142.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6 --out runmake.rsid |
| | | |
− | Looking up SNPs by rsID is possible by (for example) | + | Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position? |
− | $HK/vcf-lookup-rsid --vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --sepchr --rs rs17766217 | + | $HK/tabix $OUT/vcfs/chr8/chr8.filtered.rsid.vcf.gz 8:128504497 | less |
| * Be sure to look at the QUAL & your sample's PL, and not just the GL field. Check if QUAL is 0 or PL is 0,0,0 - NS is also probably 0; DP is probably 0. That means you probably didn't have any copies, so your GT may not be correct/is unknown. | | * Be sure to look at the QUAL & your sample's PL, and not just the GL field. Check if QUAL is 0 or PL is 0,0,0 - NS is also probably 0; DP is probably 0. That means you probably didn't have any copies, so your GT may not be correct/is unknown. |
| | | |
| If you want to browse the rsIDs of known GWAS SNPs, you can do this by | | If you want to browse the rsIDs of known GWAS SNPs, you can do this by |
− | cut -f 1,8,22 $HK/../data/gwascatalog/gwascatalog.txt | less | + | cut -f 1,8,12,13,22 $HK/../data/gwascatalog/gwascatalog.txt | grep -w rs17766217 |
| | | |
| ==== Annotating your genome ==== | | ==== Annotating your genome ==== |
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| | | |
| Or you can run multiple chromosomes in parallel in one command | | Or you can run multiple chromosomes in parallel in one command |
− | $HK/run-command-wgs --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --numjobs 6 | + | $HK/run-make --repeat-chr --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --numjobs 6 --out runmake.anno |
− |
| + | |
| ==== Extracting only exonic SNPs ==== | | ==== Extracting only exonic SNPs ==== |
| | | |
| If you want to look at the exonic SNPs, you can extract using the following command | | If you want to look at the exonic SNPs, you can extract using the following command |
− | $HK/run-command-wgs --cmd "($HK/tabix -H $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz; zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz | grep Exon;)| $HK/bgzip -c > $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz" --numjobs 6 | + | $HK/run-make --repeat-chr --cmd "($HK/tabix -H $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz; zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz | grep Exon;)| $HK/bgzip -c > $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz" --numjobs 6 --out runmake.exome |
| | | |
| And they can be combined as follows | | And they can be combined as follows |
| (zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz; zcat $OUT/vcfs/chr[2-9]/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chr??/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chrX/chrX.filtered.rsid.anno.exon.vcf.gz | grep -v ^#) | $HK/bgzip -c > $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | | (zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz; zcat $OUT/vcfs/chr[2-9]/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chr??/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chrX/chrX.filtered.rsid.anno.exon.vcf.gz | grep -v ^#) | $HK/bgzip -c > $OUT/wgs.filtered.rsid.anno.exon.vcf.gz |
| + | $HK/tabix -pvcf $OUT/wgs.filtered.rsid.anno.exon.vcf.gz |
| | | |
| ==== Exonic Variants NOT found by 1000G ==== | | ==== Exonic Variants NOT found by 1000G ==== |
Line 463: |
Line 325: |
| | | |
| Want to see this from the BAM file? Use samtools tview: | | Want to see this from the BAM file? Use samtools tview: |
− | $GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $GC/gotcloud.ref/human.g1k.v37.fa | + | $GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $REF/hs37d5.fa |
| Use 'g' & enter the Chr:Pos | | Use 'g' & enter the Chr:Pos |
| * Some patterns may indicate not real variants. | | * Some patterns may indicate not real variants. |
Line 472: |
Line 334: |
| | | |
| The phred score at the last column quantifies the degree of functional significance | | The phred score at the last column quantifies the degree of functional significance |
− |
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| | | |
| </div> | | </div> |
| </div> | | </div> |
| + | |
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