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Old 03-21-2016, 04:56 AM   #6
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Location: SZ

Join Date: Mar 2016
Posts: 7

Originally Posted by mastal View Post
I think maybe I understand a bit better now.

I think if you are running lobSTR with a paired-end bam file, you need to give it a bam file that has been name-sorted (samtools sort -n) for the -f parameter, because it needs the two reads of a pair to be next to each other in the file.

Later steps, like running allelotype, may need bam files sorted by coordinate, as shown in some of the examples where they sort the bam files that are output from running losSTR.

Hope this makes more sense.

Thank you for your reply. I agree with you, but there is something wrong with me.

When I run lobSTR with my name-sorted paired-end bam file just like what you mentioned, I get the follow warnings:

WARNING: Could not find pair for BRISCOE:4:... Is the bam file sorted by read name?

All my screen is full of the warnings. Is it nomal?

Besides, I when I run allelotype with the bam it generates, I also get the warnings in my output:

WARNING: Skipping locus chr1:123585375. Invalid period size (20)
WARNING: Discarding duplicate of locus chr1: 123587826

I don't know what it means and what should I do?

Thank you.

Last edited by Alphabets; 03-21-2016 at 05:03 AM.
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