Changes

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

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

  export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref

  export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref

  export SAMPLE=SampleXX  

  export SAMPLE=SampleXX  

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

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

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

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 --out runmake.anno --autosomes

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

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 ====