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Pindel - comparing tumour vs somatic sample

I'd like to run Pindel on some WGS datasets (tumour and normal samples) mapped using BWA-MEM. According to the user guide, I can run option 1 after creating a bam-configuration file:

./pindel -f ref.fa -i 1222config.txt -c ALL -o sample_1222

However, this would compare all the samples to the reference genome, and not to each other (e.g. tumour vs somatic sample).

To directly compare two samples, my understanding is that I'd have to create a Pindel txt file from the bam files using Bam2Pindel. Is there any way I could compare two samples without processing them with Bam2Pindel first?

snvs ngs wgs pindel
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updated by Chris Miller Chris Miller • written by Lillian • Lillian

I'll have a look, thanks!

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written by Lillian • Lillian

1 answer

Here's the outline of a script I've used to run pindel in the past"

nbam=$1
tbam=$2
outdir=$3

mkdir $outdir;
cd $outdir;
echo "$nbam    400     normal" >config
echo "$tbam     400                 tumor" >>config

fasta=/path/to/reference.fa
pindel -i config -T 4 -o pindel -f $fasta -c 13
cat pindel_* >output.pindel
pindel2vcf -p output.pindel -r $fasta -R GRCh38 -d <date> -v output.vcf -c 13 -e 3

There is also a CWL workflow for running it here: https://github.com/genome/analysis-workflows/blob/master/definitions/subworkflows/pindel.cwl

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written by Chris Miller Chris Miller

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