From Genome Analysis Wiki
Jump to navigationJump to search
76 bytes added
, 12:10, 22 May 2015
Line 263: |
Line 263: |
| 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 GC=~/seqshop/gotcloud |
| + | |
| | | |
| export SAMPLE=SampleXX | | export SAMPLE=SampleXX |
Line 278: |
Line 280: |
| | | |
| 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. |
| | | |
Line 299: |
Line 301: |
| 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 ==== |