SeqShop: Calling Your Own Genome, May 2015

Login instructions for seqshop-server

Login to the seqshop-server Linux Machine

This section will appear redundantly in each session. If you are already logged in or know how to log in to the server, please skip this section

1. Login to the windows machine
• The username/password for the Windows machine should be written on the right-hand monitor
2. Start xming so you can open external windows on our Linux machine
• Start->Enter "Xming" in the search and select "Xming" from the program list
• Nothing will happen, but Xming was started.
View Screenshot



3. Open putty
• Start->Enter "putty" in the search and select "PuTTY" from the program list
View Screenshot



4. Configure PuTTY in the PuTTY Configuration window
• Host Name: seqshop-server.sph.umich.edu
View Screenshot



• Setup to allow you to open external windows:
• In the left pannel: Connection->SSH->X11
• Add a check mark in the box next to Enable X11 forwarding
View Screenshot



• Click Open
• If it prompts about a key, click OK
5. Enter your provided username & password as provided

You should now be logged into a terminal on the seqshop-server and be able to access the test files.

• If you need another terminal, repeat from step 3.

Login to the seqshop Machine

So you can each run multiple jobs at once, we will have you run on 4 different machines within our seqshop setup.

• You can only access these machines after logging onto seqshop-server

3 users logon to:

ssh -X seqshop1

3 users logon to:

ssh -X seqshop2

2 users logon to:

ssh -X seqshop3

2 users logon to:

ssh -X seqshop4

Tuesday - Start SNP Calling

Setup Screen

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?

One solution is screen!

How do I use screen?

Before running your command, you need to start screen:

screen

As it says, press Space or Return.

• 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

export SAMPLE=SampleXX

or

export SAMPLE=NA12878

Point to your GotCloud & your output directory:

export GC=~/seqshop/gotcloud
export OUT=~/$SAMPLE/output

List of BAMs

The list of BAMs has already been created (just 1 BAM, your sample).

• But it is simply SAMPLE\tBAM_name, so easy to figure out

cat ~/$SAMPLE/output/bam.list

SampleXX SampleXX/output/bams/SampleXX.recal.bam

• 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 SNPCALL

cat ~/$SAMPLE/gotcloud.conf

You will see this:

# References
SS_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample
REF_DIR = $(SS_DIR)/ref/gotcloud.ref/

######### ALIGNMENT ########
MAP_TYPE = BWA_MEM
FASTQ_LIST = fastq.list
BATCH_TYPE = 
BATCH_OPTS = 
BWA_THREADS = -t 6

# SNP Call Settings
UNIT_CHUNK = 20000000      # Chunk size of SNP calling : 20Mb
VCF_EXTRACT = $(SS_DIR)/snpOnly.vcf.gz
MODEL_GLFSINGLE = TRUE
MODEL_SKIP_DISCOVER = FALSE
MODEL_AF_PRIOR = TRUE

EXT_DIR = $(SS_DIR)/ext
EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz

Running SNP Calling

Run GotCloud snpcall with 8 jobs running in parallel

• Why 8?
  • You want to run as many as you can.
  • 2-3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine

${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 8 --outdir $OUT

• 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.

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.

If you have not detached from screen:

Ctrl-a d

exit PuTTY

FEEDBACK!

Please provide feedback on today:

https://docs.google.com/forms/d/1ADTkBjzT-QNj2lrejyqGqDaahTponrw20kSgDNwqwH4/viewform

Thursday

Checking if snpcall Completed

Resume screen to Check Jobs

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.

Verify you got a "completed successfully" message.

How long did snpcall calling take? Look at the log message - time in seconds.

List of BAMs

The list of BAMs has already been created (just 1 BAM, your sample).

• But it is simply SAMPLE\tBAM_name, so easy to figure out

cat ~/$SAMPLE/output/bam.list

SampleXX SampleXX/output/bams/SampleXX.recal.bam

• 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 INDEL Configuration

cat ~/$SAMPLE/gotcloud.conf

Same as it looked the other day with no special Configuration settings for INDEL calling.

Running INDEL

Run GotCloud indel with 6 jobs running in parallel

${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 --outdir $OUT

• 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.

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

FEEDBACK!

Please provide feedback for today. https://docs.google.com/a/umich.edu/forms/d/1iES6usHxLB7Ec9hRxtqYgH7v05lU3Ume4VJcksx8Ogg/viewform

Friday

SeqShop: Ancestry On Your Own Genome, May 2015

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

Point to your GotCloud & your output directory:

export GC=~/seqshop/gotcloud
export OUT=~/$SAMPLE/output

Reviewing Indel Results

Look in the output directory

ls ~/$SAMPLE/output

What in that directory was produced by indel calling?

• gotcloud.indel.conf
  • dump of all configuration settings for this run
• gotcloud.indel.Makefile
  • Makefile that was generated to manage all of the commands to be run
• gotcloud.indel.Makefile.log
  • log of all commands run by the Makefile
• indel/
  • indel output directory

Let's look at the indel output

ls ~/$SAMPLE/output/indel 

• 3 directories
  • aux - intermediate files
  • indelvcf - intermediate files
  • final indel files

Final indel directory:

ls ~/$SAMPLE/output/indel/final

• all.genotypes.vcf.gz - output VCF
• all.genotypes.vcf.gz.tbi - output VCF index file to allow jumping to positions
• all.genotypes.vcf.gz.tbi.OK - completion indicator
• merge/ - directory with per chromosome bcf (binary vcf) files
• all.genotypes.vcf.gz.OK - completion indicator
• all.genotypes.vcf.gz.tbi.log - log
• concat.log - log

Looking at final INDEL VCF

Note that because this is a single sample calling, many of the INFO fields are less meaningful as many of the values like HWE p values, allele frequencies, inbreeding coefficient are a function of a population. Nonetheless, we may examine the results. First, we see how many indels were discovered for your genome:

$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz 

      no. Indels                         :     588566
          2 alleles (ins/del)            :          588566 (0.87) [273261/315305]

This gives use 588,566 indels with an insertion deletion ratio of 0.87.

We next look at the filtered set. The PASS filter reduces the setof indels to a non overlapping set and the INFO.AC!=0 extracts all indels that are either heterozygous or homozygous alternative. Some indels that were originally discovered were found to be the homozygous reference genotype. Invariably, these are relative high depth calls where the alternative allele is discovered less or is mis-specified.

$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AC!=0"

      no. Indels                         :     549963
          2 alleles (ins/del)            :          549963 (0.91) [261480/288483]

About 38K indels were removed, the insertion deletion ratio increases to 0.91. Note that in general, for high depth data, discovered indels are reported with insertion deletion ratios close to 1. So this is a good sign. Next generation sequencing errors are bias for deletions.

It is possible to perform a slightly more stringent filtering using allele balance. The allele balance estimator in this case is meaningful still for an individual because it is a function of read depth. Note that AB>0.5 denotes reference bias and AB<0.5 denotes alternative allele bias.

$GC/bin/vt peek ~/$SAMPLE/output/indel/final/all.genotypes.vcf.gz -f "PASS&&INFO.AC>0&&INFO.AB<0.7&&INFO.AB>0.3"

      no. Indels                         :     490965
          2 alleles (ins/del)            :          490965 (0.92) [235254/255711]

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

Look in the output directory

ls ~/$SAMPLE/output

Look at the vcfs:

ls ~/$SAMPLE/output/vcfs

Friday : More SNP Analysis

In addition, set another environmental variable for locating the binaries for custom analysis

export HK=/net/seqshop-server/home/hmkang/apigenome/bin
export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/
export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref
export GC=~/seqshop/gotcloud

export SAMPLE=SampleXX 
export OUT=~/$SAMPLE/output

Annotation / Lookup against dbSNP

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_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

$HK/run-make --repeat-chr --cmd "$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, rs17766217) -- How can we find its position?

$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.

If you want to browse the rsIDs of known GWAS SNPs, you can do this by

cut -f 1,8,12,13,22 $HK/../data/gwascatalog/gwascatalog.txt | grep -w rs17766217

Annotating your genome

You can annotate your genome using EPACTS software packages. Individual chromosome can be annotated by running.

$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz

Or you can run multiple chromosomes in parallel in one command

$HK/run-make --repeat-chr --cmd "$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

If you want to look at the exonic SNPs, you can extract using the following command

$HK/run-make --repeat-chr --cmd "($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

(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

If you are interested in rare variants that are not identified by 1000G, you can extract them by running

zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | less

For example,

zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | perl -lane 'print "$1\t$F[6]" if ( /ANNO=([^;:]+)/)' | sort | uniq -c

will give you the counts of variants, separate by the filtering results

• Q1. How manny novel silent, missense, and nonsense SNPs are found? Is that too few, too small, or just about right?
• Q2. Looking at each functional category, which functional categories has largest fraction of SNPs failed filter? Why do you think it is?
• Q3. Can you exclude the sites that are also in dbSNP, and count how many nonsense variants are left?

To also exclude those in dbsnp:

zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" | grep -v rs| perl -lane 'print "$1\t$F[6]" if ( /ANNO=([^;:]+)/)' | sort | uniq -c

Exclude dbsnp and look at Stop_Gain variants

zcat $OUT/wgs.filtered.rsid.anno.exon.vcf.gz | grep "EXTFILTER=NA,NA" | grep -v -w "0/0" |grep -v rs | perl -lane 'print "$_" if ( /ANNO=Stop_Gain/)' |grep -w PASS

Want to see this from the BAM file? Use samtools tview:

$GC/bin/samtools tview $SAMPLE/output/bams/$SAMPLE.recal.bam $REF/hs37d5.fa

Use 'g' & enter the Chr:Pos

• Some patterns may indicate not real variants.

If you want to know predicted functional significance of a particular variant, you can search by

$HK/tabix $HK/../data/CADD/whole_genome_SNVs.tsv.gz [chr]:[pos] | head -3

The phred score at the last column quantifies the degree of functional significance

OVERALL COURSE FEEDBACK!

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