Tag Archives: samtools

missing SAM header with minimap2 and samtools

Tweet When using minimap2 to map sequencing reads onto a reference, you can use this kind of command (be careful, this is wrong as you will see later):

The command is verbose and prints this kind of information. Note … Continue reading

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failed to convert from cram to bam (parse error CIGAR character)

Tweet In order to convert a bioinformatic file from CRAM to BAM format, I naively used the samtools command available on a cluster but got this error:

After a few commands trying to fix the issue, I realised that … Continue reading

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