Question: VCF - InDels and SNPs relation
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gravatar for bwczech
14 days ago by
bwczech70
bwczech70 wrote:

Hi, I have files with my SNPs and InDels. Do you have any idea how to check whether indels are called mainly in the vicinity of SNPs or not? How can I check it and calculate this relation? Thank you for your all proposition.

snp vcf indel • 96 views
ADD COMMENTlink modified 14 days ago by Pierre Lindenbaum120k • written 14 days ago by bwczech70
0
gravatar for Pierre Lindenbaum
14 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

you could used bedtools closest to get a distribution of the distances indel/snp

for T in snps indels 
do
bcftools view -G -v $T  inputvcf.gz |  bcftools query --format "%CHROM\t%POS\t%END\n" | sort -T. -t $'\t' -k1,1 -k2,2n > $T.bed
done

bedtools closest -a indels.bed -b snps.bed -d | cut -f 7 | sort -n
ADD COMMENTlink written 14 days ago by Pierre Lindenbaum120k

wow! Thank you, I did not know this site of bedtools.

How can I understand zeros? That''s mean that SNP is inside indel?

ADD REPLYlink modified 14 days ago • written 14 days ago by bwczech70

How can I understand zeros? That''s mean that SNP is inside indel?

yes

ADD REPLYlink written 14 days ago by Pierre Lindenbaum120k
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