Hi,
I have a bam file that I have run through the GATK pipeline (i.e. de novo realignments around indels, duplicates removed and quality recalibration). I then wish to run mpileup on the processed bam files using the command:
samtools mpileup -s -f hg19.fa.fai sample.sorted.bam > sample.pileup
The programme seems to work initially but then aborts saying:
samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed.
I haven't learned to programme in C so am really struggling to understand what this means and how I can circumvent the issue. Can anyone help?
NB The original sequencing was done with Complete Genomics so I have had to convert from their proprietary alignment formats to bam using cgatools
I have a bam file that I have run through the GATK pipeline (i.e. de novo realignments around indels, duplicates removed and quality recalibration). I then wish to run mpileup on the processed bam files using the command:
samtools mpileup -s -f hg19.fa.fai sample.sorted.bam > sample.pileup
The programme seems to work initially but then aborts saying:
samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed.
I haven't learned to programme in C so am really struggling to understand what this means and how I can circumvent the issue. Can anyone help?
NB The original sequencing was done with Complete Genomics so I have had to convert from their proprietary alignment formats to bam using cgatools
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