User: vctrm67
vctrm67 • 10
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Posts by vctrm67
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... I have generated a callset of mutations, based on a gene panel, from GATK's Mutect using a panel of normals. However, I am trying to eliminate called mutations that don't lie within the coverage of the panel (comprised of WES samples) as the panel may not cover areas where there are reads in the gen ...
written 4 days ago by
vctrm67 • 10
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... Posting here because the GATK forums are slow to respond.
To my understanding, BaseRecalibrator requires certain fields, of which includes the platform information. I received bam files in which I do not see any information regarding the platform. Is there a way to add this in? I looked at AddorRe ...
written 9 days ago by
vctrm67 • 10
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... I think my problem has more so to do with that the reference hg19 includes contigs beyond the unmapped sequences that aren't reflected in what the BAM file is aligned with. As you can see, the list of contigs for the reference is longer than the list of contigs for the reads. ...
written 11 days ago by
vctrm67 • 10
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... Oh. Do you know if this is hg19 then? I tried running some GATK tools but I get an error message that looks like:
##### ERROR MESSAGE: Input files reads and reference have incompatible contigs. Please see http://gatkforums.broadinstitute.org/discussion/63/input-files-have-incompatible-contigsf ...
written 11 days ago by
vctrm67 • 10
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... Does anyone know which version of hg19 this is based on the sequence contigs in the bam file header?
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:1591 ...
written 11 days ago by
vctrm67 • 10
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Comment:
C: Error in posting to Biostars?
... I tried, and it did not work, so I posted this question in the same manner. ...
written 12 days ago by
vctrm67 • 10
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... I'm trying to post a question to biostars but I'm getting this error message:
`Language "cy" is not one of the supported languages ['en']!`
Does anyone know what this means? I wasn't aware of any language restriction and my post is in English. I commented some code too, but I don't know what it ...
written 12 days ago by
vctrm67 • 10
• updated
11 days ago by
Istvan Albert ♦♦ 82k
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... I am getting an error message with regards to a corrupt bam:
```
Error: BAM file is corrupt. Samtools cannot parse header
```
Does anyone know if there is a fix? Or do I have to realign the bam file?
...
written 12 days ago by
vctrm67 • 10
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... No I received this through many different people and it is difficult to contact the originators ...
written 12 days ago by
vctrm67 • 10
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... Wouldn't I just look for intervals that have coverage? Wouldn't those be the "relevant intervals"? ...
written 12 days ago by
vctrm67 • 10
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