BAM validation problems (also re: Picard)

[brantfaircloth]

On BAM output files from ngm (which is great so far, btw!), Picard reports (when adding RG to or validating the BAM):

Mapped mate should have mate reference name

For the moment, this error can be worked around using:

java -Xmx30g -jar \
~/bin/FixMateInformation.jar \
I=<input>.bam \
O=<output>.bam \
VALIDATION_STRINGENCY=LENIENT

But it would be excellent to get valid BAM straightaway on output from ng.

[philres]

Hi Brant,

thank you very much for the feedback! We'll look into this and fix it in the next version of NextGenMap (which we are planing to release this month).

If you have any other suggestions don't hesitate to contact us.

Best,
Philipp