1. Community
2. Germline
3. output BAM form ApplyBQSR query using --interval option

Thanks a lot for this, Genevieve Brandt (she/her)! It was really helpful.

• View comment
• prasundutta87
• February 10, 2021 20:07
• 0 votes

1. Community
2. Germline
3. output BAM form ApplyBQSR query using --interval option

Hi,I think this is what happened. After visualising a very small exonic portion from hg38, I observed that ApplyBQSR removed reads outside the exonic region. Please see the attached picture. Howeve...

• View comment
• prasundutta87
• February 10, 2021 11:42
• Edited
• 0 votes

1. Tool Index
2. 4.1.9.0
3. BaseRecalibrator

Hi Bhanu, Thanks for your reply. Sorry, I was'nt clear with my question. I was going through some old documents on how to confirm if BQSR has worked well. In most of the documents, a second recalib...

• View comment
• prasundutta87
• February 07, 2021 12:04
• 2 votes

1. Tool Index
2. 4.1.9.0
3. BaseRecalibrator

Hi, There was a -bqsr option in old version of BaseRecalibrator. In order to produce a second recalibration table, you could give the first recalibration table to it along with the original BAM fil...

• View comment
• prasundutta87
• February 06, 2021 17:42
• 0 votes