Question

question about pindel

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11.1 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 • 2.5k views

ADD COMMENT • link updated 3.8 years ago by Ram 45k • written 11.1 years ago by hnmcy11 ▴ 10

Ram · Answer 1 · 2014-09-20

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11.1 years ago

liangkaiye ▴ 250

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

Kai

ADD COMMENT • link updated 3.8 years ago by Ram 45k • written 11.1 years ago by liangkaiye ▴ 250

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

ADD REPLY • link updated 3.8 years ago by Ram 45k • written 11.1 years ago by hnmcy11 ▴ 10