Question

question about pindel

0

Entering edit mode

10.2 years ago

hnmcy11 ▴ 10

I have bams at hand and want to call deletions with pindel. Since the aligner I used is Novoalign, it seems that sam2pindel is essential for reads extraction according to the manual. So I wonder whether can I use pindel command directly rather than sam2pindel? And I notice that read name should begin with @, is that a must? Thanks in advance!

sequencing next-gen • 2.2k views

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by hnmcy11 ▴ 10

Ram · Answer 1 · 2014-09-20

1

Entering edit mode

10.2 years ago

liangkaiye ▴ 250

You can directly use bam as input, -i config.

Kai

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by liangkaiye ▴ 250

0

Entering edit mode

Thanks! And can I analyse single-end bams with Pindel?

ADD REPLY • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by hnmcy11 ▴ 10