Get Insertion / Deletion Count From Vcf
I have a VCF file and I wanted to get only the count for insertion and deletions identified in the VCF. Is there any way to simply output the count of insertions and deletions from a VCF file?
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Alex Reynolds
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win
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win
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In BEDOPS 2.4 and greater, you can do the following to get the counts of the number of single nucleotide variants:
$ vcf2bed --snvs < myVariants.vcf | wc -l
To get the number of insertions:
$ vcf2bed --insertions < myVariants.vcf | wc -l
And the number of deletions:
$ vcf2bed --deletions < myVariants.vcf | wc -l
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Alex Reynolds
vcfstats provides one simple method to do so. You can also generate length-frequency distributions using vcflengthdelta (also in vcflib).
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Erik Garrison
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