inconsistent quality strings in error free sam file

[jazberna1]

Hello Yunfei,

This is probably an ART question rather than varsim but I have noticed that if you generate an error free sam by passing --art_options="--errfree" to varsim the generated sam file has inconsistent quality strings with different lengths than the corresponding reads. This causes errors 'samtools fastq' or 'gatk SamToFastq'.

Jorge

[yunfeiguo]

Hi @jazberna1 you are right, I did see inconsistent SEQ and QUAL lengths in ART's errFree.sam file. I think a workaround would be ignore the quality scores and convert to FASTA, e.g.

perl -ane 'if(!/^@/){print ">$F[0]\n$F[9]\n"}' errFree.sam