From Genome Analysis Wiki
Jump to navigationJump to search
451 bytes removed
, 17:19, 12 December 2009
Line 5: |
Line 5: |
| Here is an example of how <code>vcfCodingSnps</code> works: | | Here is an example of how <code>vcfCodingSnps</code> works: |
| | | |
− | vcfCodingSnps -s chrom1-CHB.vcf -g genelist.txt -o annotated-chrom1-CHB.vcf | + | vcfCodingSnps -s chrom22-CHB.vcf -g genelist.txt -o annotated-chrom22-CHB.vcf |
| | | |
| == Command Line Options == | | == Command Line Options == |
Line 31: |
Line 31: |
| 22 14441250 . t c 59 mapQ=0 depth=40 GT:GQ:DP 1|1:56:25 1|1:31:15 1|1:32:0 | | 22 14441250 . t c 59 mapQ=0 depth=40 GT:GQ:DP 1|1:56:25 1|1:31:15 1|1:32:0 |
| 22 14443154 . t g 45 mapQ=9 depth=92;duples=homs;mac=2 GT:GQ:DP 1|1:49:21 0|0:60:20 1|0:100:51 | | 22 14443154 . t g 45 mapQ=9 depth=92;duples=homs;mac=2 GT:GQ:DP 1|1:49:21 0|0:60:20 1|0:100:51 |
− | 22 14446720 . c t 52 mapQ=0 depth=81;duples=homs;mac=2 GT:GQ:DP 1|1:23:31 0|0:23:34 1|0:76:16 | + | ... ... |
− | 22 14446721 . a g 49 mapQ=0 depth=82;duples=homs;mac=2 GT:GQ:DP 1|1:21:30 0|0:21:36 1|0:100:16
| |
− | 22 14449771 . g a 78 mapQ=27 depth=68;mac=1;tdt=1/1 GT:GQ:DP 1|0:64:21 0|0:75:36 1|0:28:11
| |