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Picard Library: H And B Types

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.

picard
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updated by nilshomer • nilshomer • written by ranlib • ranlib

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

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

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.

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written by nilshomer • nilshomer

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