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Summary
First you want to know what is in the vcf file.
${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz
stats: no. of samples : 62
We can count the number of variants with different filters with the following commands.
${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS"
stats: no. of samples : 62
no. of chromosomes : 1 <br>
no. Indels : 584583 2 alleles (ins/del) : 584 583 (0.69) [239/345344]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.overlap"
stats: no. of samples : 62
no. of chromosomes : 1 <br>
no. Indels : 136137 2 alleles (ins/del) : 136 137 (1.8985) [89/4748] #notice the difference in insertion deletion ratios
>=3 alleles (ins/del) : 0 (-nan) [0/0]
#passed singletons only
${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&INFO.AC==1"
#passed indels of length 1 only
${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&LEN==1"
#passed indels of length >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
${GC}/bin/vt peek ${OUT}/indel/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)"
=== Comparison with other data sets ===

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