Dear everyone, I am using
$ samtools view -h -F 4 input.bam > input_only_mapped.sam to filter out unmapped reads from my bam file. However, this command does not affect the header section. I would like to remove reference sequences without any alignments from the header, as well (The reason is, the number of the lines in the header section exceeds the limit of a downstream program. This is stemming from the reference file I use to make the alignments, but I have no other options). So, I am wondering whether it is possible to remove reference sequences that are not mapped by any reads from the header section? Any help is greatly appreciated. Thank you in advance, Best regards, Ani Akpinar
------------------------------------------------------------------------------
_______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
