Question: Picard tools - Cigar element being constructed with negative length
0
gravatar for Andy
12 days ago by
Andy20
Andy20 wrote:

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

snp rna-seq alignment • 123 views
ADD COMMENTlink modified 8 days ago by finswimmer7.0k • written 12 days ago by Andy20
1

output of

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

?

ADD REPLYlink written 12 days ago by Pierre Lindenbaum114k

Apologies for late reply.

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

Any ideas?

Regards

Andy

ADD REPLYlink modified 8 days ago • written 8 days ago by Andy20

any ideas ?

try to isolate the read with the problem...

ADD REPLYlink written 8 days ago by Pierre Lindenbaum114k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1398 users visited in the last hour