Problem Running Pindel With Bam Files

Question

[xenophiliuslovegood]

Hi, I am running Pindel version 0.2.4p, March 26 2012, on a set of BAM files. It chokes on them, printing out:

No currentState.Reads for chr3 in file.bam

(Note that the BAM files themselves were not produced by BWA, but by another mapper).

Since I could not use the BAM files I tried to generate the input to PINDEL by running sam2pindel on the corresponding set of SAM files, but this attempt was also unsuccessful (output file generated by sam2pindel is empty).

1)Has any of you encountered the same kind of difficulty? If so, how did you fix the problem? In particular, 2)Is it possible to generate BAM files compatible with PINDEL if one is not using BWA?

Answer 1

[Raymond301]

I've used Novo Align successfully.

There is one thing to note....Pindel will not work on Single End reads! Ensure that you're alignment contains paired reads.

java -jar picard/1.55/CollectInsertSizeMetrics.jar I=<sorted.bam> H=<output histogram.png> O=<output stats.txt>

samtools view <sorted.bam> | sam2pindel - <pindel.txt> <insert size from output stats.txt> <prefix> 0 Illumina-PairEnd <or Mate-Pair>

pindel -f <hg ref> -p <pindel.txt> -c ALL -o <prefix>

pindel2vcf -p <prefix>_<suffix> -r <hg ref> -R 1000GenomesHg19 -d <unix date>

<suffix> = _D, _BP, _INV, _SI, _LI, _TD : Then merge or concat the vcfs.

-- I don't know if this explains your error, but I do know it is possible to use Pindel on other aligners.

[xenophiliuslovegood]

Thanks for the effort : my alignment did contain paired end alignments, though. I solved my problem simply by inserting an @RG field in the BAM file. Things seem to work now, but I have still to check if the output makes sense.

[Raymond301]

Ah, that would do it. I'm sorry I couldn't be more help.