Picard tools - Cigar element being constructed with negative length

Question

[Andy]

Hi

I am trying to mine SNPs using Star 2-pass / GATK using the process outlined here.

https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq

I've run the two passes of STAR, but I'm getting an error during the picard processing step.

When I run this command;

java -jar /home/XXXXXX/XXXX/bin/picard.jar AddOrReplaceReadGroups I=Aligned.out.sam O=rg_added_sorted.bam SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample

I get the following error:

Exception in thread "main" java.lang.IllegalArgumentException: Cigar element being constructed with negative length: -65 and operation: D

Any ideas where I'm going wrong?

Thanks.

Andy

[Pierre Lindenbaum]

output of

grep -v '^@' Aligned.out.sam  | cut -f 6 | grep -F 'D'  | grep -m1 -F '-'

?

[Andy]

Apologies for late reply.

I don't get any output when I try the above command.

Any ideas?

Regards

Andy

[Pierre Lindenbaum]

any ideas ?

try to isolate the read with the problem...