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How To Retrieve Reads Supporting A Snp/Indel

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I used samtools and varscan for variant calling like this:

samtools mpileup \
  -f genome.fa \
  tku.sorted.rmdup.bam \
  | java -jar VarScan.v2.3.5.jar pileup2snp \
  --min-coverage 8 \
  --min-reads2 2 \
  --min-avg-qual 15 \
  --min-var-freq 0.01 \
  --p-value 0.001 \>tku.snp.vcf

now I want to retrieve all the reads supporting a specific SNP/indel and calculate the distribution of SNP/indel on the sequenced reads, is there any tools or proper way to achieve this?


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