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Old 03-20-2016, 05:06 PM   #3
Alphabets
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Location: SZ

Join Date: Mar 2016
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Quote:
Originally Posted by mastal View Post
The --rg-sample and --rg-lib parameters should be tags with read-group information, not the bam files.

See the lobSTR FAQs for more info.

http://melissagymrek.com/lobstr-code/faq.html

I think if you start with a bam file rather than fastq files then it should be sorted and indexed. Note that the command line options description for --bampair says that the file should be sorted by name order, 'samtools sort -n'.
I know what you mean, the --rg-sample and --rg-lib parameters should not be the bam files. But I am confused of the third line "-f my_sample.bam --bampair". I think the -f parameter should be the sorted bam not the raw bam. The document shows it is the raw bam not the sorted bam file,which confuse me.

the document is:
http://melissagymrek.com/lobstr-code...html#pairedbam
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