Extract SNPs within 5 bps distance apart

Question

[waqasnayab]

Hi,

I am wondering is there a way to extract / print those variants from a vcf file whose distance is not more than 5 bps apart?

Regards,

Waqas.

Answer 1

[Pierre Lindenbaum]

If I'm not wrong, you can flag the close SNPs with: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php

java -jar /commun/data/packages/gatk/3.7.0/GenomeAnalysisTK.jar -T VariantFiltration -R ref.fasta -V input.vcf --clusterSize 2 --clusterWindowSize  5

this will add 'SnpCluster' in the FILTER column.

[waqasnayab]

Yes, Pierre GATK's VariantFiltration worked for me. I wanted the exact same thing...,,,!!!!

Big Thanks...,,,,!!!!

Cheers,

Waqas.

Answer 2

[Matteo Schiavinato]

Yes, you can do it in many ways (python, command line, perl). You just have to ask for this condition to be verified:

for each line, print line if (line_position - previous_line_position) <= 5

The position field in the VCF file is the 2nd :) https://samtools.github.io/hts-specs/VCFv4.2.pdf

[waqasnayab]

yeah, chromosomal positions (second column) is my target. I searched on google but I failed. Is there a way, to do the same in awk?

Thanks,

Waqas.

[Pierre Lindenbaum]

yes, but it's more complicated with indels/multi-allelic sites + check the chromosome is the same.

Answer 3

[sacha]

I guess you can do it with bedtools cluster in two step. http://bedtools.readthedocs.io/en/latest/content/tools/cluster.html?highlight=cluster