Picard Library: H And B Types

Question

[ranlib]

I need to read bam files with H and B types in them with software that uses an older Picard library which doesn't handle those yet. Anyone know of a good way to filter those types out?

Thanks.

[Pierre Lindenbaum]

what is 'types' ? a SAM flag ? what is the B flag ? Why cannot you use a newer picard ibrary ?

Answer 1

[nilshomer]

You could convert the file from BAM to SAM, then use your favorite language to remove the offending tags from each line (sed, awk, perl, python, and even Samtools only C library), and then finally convert back to BAM. The rest is left as an exercise to the reader.