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Question: VCF - InDels and SNPs relation
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gravatar for bwczech
7 months ago by
bwczech • 90
bwczech • 90 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 • 301 views
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modified 7 months ago by Pierre Lindenbaum ♦ 124k • written 7 months ago by bwczech • 90
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gravatar for Pierre Lindenbaum
7 months ago by
Pierre Lindenbaum ♦ 124k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 124k 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 COMMENT • link written 7 months ago by Pierre Lindenbaum ♦ 124k

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 REPLY • link modified 7 months ago • written 7 months ago by bwczech • 90

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

yes

ADD REPLY • link written 7 months ago by Pierre Lindenbaum ♦ 124k
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