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| First you want to know what is in the vcf file. | | First you want to know what is in the vcf file. |
| | | |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz |
| | | |
| stats: no. of samples : 62 | | stats: no. of samples : 62 |
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| We can count the number of variants with different filters with the following commands. | | We can count the number of variants with different filters with the following commands. |
| | | |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS" | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS" |
| | | |
| stats: no. of samples : 62 | | stats: no. of samples : 62 |
| no. of chromosomes : 1 <br> | | no. of chromosomes : 1 <br> |
− | no. Indels : 584 | + | no. Indels : 583 |
− | 2 alleles (ins/del) : 584 (0.69) [239/345] | + | 2 alleles (ins/del) : 583 (0.69) [239/344] |
| >=3 alleles (ins/del) : 0 (-nan) [0/0] | | >=3 alleles (ins/del) : 0 (-nan) [0/0] |
| | | |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.overlap" | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.overlap" |
| | | |
| stats: no. of samples : 62 | | stats: no. of samples : 62 |
| no. of chromosomes : 1 <br> | | no. of chromosomes : 1 <br> |
− | no. Indels : 136 | + | no. Indels : 137 |
− | 2 alleles (ins/del) : 136 (1.89) [89/47] #notice the difference in insertion deletion ratios | + | 2 alleles (ins/del) : 137 (1.85) [89/48] #notice the difference in insertion deletion ratios |
| >=3 alleles (ins/del) : 0 (-nan) [0/0] | | >=3 alleles (ins/del) : 0 (-nan) [0/0] |
| | | |
| #passed singletons only | | #passed singletons only |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&INFO.AC==1" | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&INFO.AC==1" |
| | | |
| #passed indels of length 1 only | | #passed indels of length 1 only |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&LEN==1" | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&LEN==1" |
| | | |
| #passed indels of length >4 | | #passed indels of length >4 |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&LEN>4" | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&LEN>4" |
| | | |
| #passed singletons of length 4 or insertions of length 3 | | #passed singletons of length 4 or insertions of length 3 |
− | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)" | + | ${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)" |
| | | |
| === Comparison with other data sets === | | === Comparison with other data sets === |