Question

Extract variability between coordinates

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9.5 years ago

egustavsson ▴ 10

Hi all,

Could anyone suggest how to extract variability within a range, i.e. candidate regions, from multiple vcf files?

I have exome data from a number of samples, as well as SNP array data, and I'm looking for recessive variability from the exome data within generated runs of homozygosity.

Thanks for your time

vcf genotyping-array exome variant • 1.9k views

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.5 years ago by egustavsson ▴ 10

Ram · Answer 1 · 2015-05-20

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9.5 years ago

Ashutosh Pandey 12k

Tabix can help you if you are looking for variants in a given genomic region (http://samtools.sourceforge.net/tabix.shtml)

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.5 years ago by Ashutosh Pandey 12k

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Thanks Ashutosh, tabix will do exactly what I'm looking for.

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by egustavsson ▴ 10

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Ok great. Moving it to answer.

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by Ashutosh Pandey 12k