Pindel - comparing tumour vs somatic sample

Question

[Lillian]

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?

[Matthias Zepper]

Unfortunately, I can't help you with Pindel, but at least Strelka is able to do what you want - in case switching the software is an option. (The latter is also part of the Sarek pipeline in case you wish to conveniently run an exhaustive tumor vs somatic sample analysis according to the standard of the Swedish Barntumörbanken).

[Lillian]

I'll have a look, thanks!

Answer 1

[Chris Miller]

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