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Revision as of 01:22, 6 December 2014
, 01:22, 6 December 2014→Summary
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
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 ===
