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Forum: The Pipeline 11-11-2014, 04:59 PM
Replies: 5
Views: 5,264
Posted By yuelincoln
@westerman, thanks. Below is the results. $...

@westerman, thanks. Below is the results.
$ /usr/local/software/samtools-0.1.13/samtools view ./301-10.rmdup.bam | cut -f 3 | grep chr | uniq -c | more
3175288 chrM
568694 chr1
459726 chr2
...
Forum: The Pipeline 11-10-2014, 08:51 PM
Replies: 5
Views: 5,264
Posted By yuelincoln
I think fasta file order is right, because if i...

I think fasta file order is right, because if i directly use GATK to call snp of the same bam file, all run seemed ok. But if use this file to run BaseRecalibrator, it will report this error.
So it...
Forum: The Pipeline 11-10-2014, 05:22 AM
Replies: 5
Views: 5,264
Posted By yuelincoln
How to deal with this problem? Reordersam treat bam file

##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message...
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