unclear about walt bam -> mr

[Kyle Hernandez]

Hello if I have WALT bams for use with other analyses, what settings do I need to use in to_mr to convert the WALT bam to mr format? I used general, but it seems to set the number of mismatches to 0 universally.

Kyle

[Meng Zhou]

Because the "general" option assumes minimal information from the input, the number of mismatches per read is not kept. You can filter for the NM tag in the WALT output SAM file for the mismatch.

Best regards,
Meng

On Thu, Aug 31, 2017 at 12:14 PM, Kyle Hernandez <kmher...@gmail.com> wrote:

Hello if I have WALT bams for use with other analyses, what settings do I need to use in to_mr to convert the WALT bam to mr format? I used general, but it seems to set the number of mismatches to 0 universally.

Kyle

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