Changes

  export HK=/net/seqshop-server/home/hmkang/apigenome/bin

  export HK=/net/seqshop-server/home/hmkang/apigenome/bin

  export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/

  export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/

==== Annotation / Lookup against dbSNP ====

==== Annotation / Lookup against dbSNP ====

Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position?  

Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position?  

  $HK/tabix ~/NA12878/output/vcfs/chr8/chr8.filtered.rsid.vcf.gz 8:128504497 | less

  $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.

Or you can run multiple chromosomes in parallel in one command

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

  $HK/run-make --repeat-chr --cmd "$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

==== Exonic Variants NOT found by 1000G ====

==== Exonic Variants NOT found by 1000G ====

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.

   

   

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