Hello,
After mapping Nanopore reads to reference genome with ngmlr, I converted the output to .bam with samtools and found that some part of information about mapping in CIGAR string was lost.
I tried to map again with using --bam-fix function of ngmlr, and now I don't really understand how to process my output .sam files (I am going to search for structural variations).
I tried to convert these fixed .sam files to .bam with samtools, and received an error:
[W::sam_read1] Parse error at line 347854
[main_samview] truncated file.
Which software I can proceed my data? Maybe there is another data format for long read data I don't know?
Many thanks, Anastasiia
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written
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anastasiia.satyr •
1 answer
Make sure you're using the most recent version of samtools, as support for very high numbers (>64k) of CIGAR operations was only relatively recently added to the BAM specification. Alternatively, use the CRAM format.
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written
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Devon Ryan
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