Hi,
I am quite new to NGS data here and I work with a commercial software from CLCbio which also offers a mapping algorithm of its own, called Genomic Workbench.
I would want to convert my SAM output from the software to BAM to allow using the samtools function like pileup.
I get the following error when i ran the command in Ubuntu OS
>./samtools view -huS -o DATA/test.bam DATA/s_2_1_sequence_SS200_LAwMM.sam
[samopen] SAM header is present: 24 sequences.
Parse error at line 113: CIGAR and sequence length are inconsistent
Aborted
I read somewhere in this thread that currently the samtools does not allow sam file processing without the reference sequence, so is the whats giving the problem? If so can anyone point me to a place to generate the correct reference sequence file, I tried reading through the manual but there is nowhere telling me how the reference file should be formatted. And I am looking at the whole human reference genome with 24 gbk files from NCBI.
Any help is appreciated.
Thanks
Sol
I am quite new to NGS data here and I work with a commercial software from CLCbio which also offers a mapping algorithm of its own, called Genomic Workbench.
I would want to convert my SAM output from the software to BAM to allow using the samtools function like pileup.
I get the following error when i ran the command in Ubuntu OS
>./samtools view -huS -o DATA/test.bam DATA/s_2_1_sequence_SS200_LAwMM.sam
[samopen] SAM header is present: 24 sequences.
Parse error at line 113: CIGAR and sequence length are inconsistent
Aborted
I read somewhere in this thread that currently the samtools does not allow sam file processing without the reference sequence, so is the whats giving the problem? If so can anyone point me to a place to generate the correct reference sequence file, I tried reading through the manual but there is nowhere telling me how the reference file should be formatted. And I am looking at the whole human reference genome with 24 gbk files from NCBI.
Any help is appreciated.
Thanks
Sol
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