Get Insertion / Deletion Count From Vcf
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10.4 years ago
win ▴ 970

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?

vcf • 8.5k views
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Line representing indel has a "INDEL" tag in most of the vcf files. You now have to compare the reference sequence and alternate sequence to find out if the variant is an insertion or deletion.

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10.4 years ago

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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10.4 years ago
Erik Garrison ★ 2.4k

vcfstats provides one simple method to do so. You can also generate length-frequency distributions using vcflengthdelta (also in vcflib).

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