Errors in mapping cancer exome data

[bnfoguy]

I am trying to map the reads from the ERP000703 study (http://www.ncbi.nlm.nih.gov/sra/ERX013480). I am using stampy to do the paired end mapping and when I execute the script with the following command:

./stampy.py -g hg18 -h hg18 -M /home/xxxxx/stampy-1.0.17/FastQ/CancerReads/ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/ERP/ERP000/ERP000703/ERR035488/ERR035488_1.fastq ERR035488_2.fastq > ERR035488_1_2.sam

The script will run for about two hours and then abruptly crashes. When I try to conver the sam output to an unsorted bam file, I get an error saying "Parse error at line 1921134: CIGAR and sequence length are inconsistent" > aborted.

Can someone advise me on troubleshooting this?

Thanks,

[dpryan]

Have you looked at the mentioned line in the SAM output to ensure that the CIGAR and sequence length agree? That would seem to be the obvious first step.