1. Community
2. Germline
3. Calling variants on chromosome Y

"I was thinking: should I exclude reads aligned to the pseudo genes of chromosome Y from the BAM files and then run the genotyping part of the pipeline to see if this makes a difference?" I don't t...

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• Derek Caetano-Anolles
• February 26, 2020 16:18
• 1 vote

1. Community
2. Germline
3. Calling variants on chromosome Y

So, if I'm understanding correctly, the depth for one of the y chromosome genes only has coverage in the male samples, which is what we should expect. That's good, but it doesn't tell us...

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• Derek Caetano-Anolles
• February 25, 2020 15:04
• 1 vote

1. Community
2. Other
3. HaplotypeCaller produces very large .idx files

Great! I'm glad it works! :)

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• Derek Caetano-Anolles
• February 25, 2020 10:56
• 0 votes

1. Community
2. Germline
3. Calling variants on chromosome Y

Hi Damian, I don't believe that HaplotypeCaller plays very nice with chrY, so it may be most expedient to just exclude them from the female analysis (if you're certain they don't actually have Y ch...

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• Derek Caetano-Anolles
• February 24, 2020 18:07
• 1 vote

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2. Other
3. HaplotypeCaller produces very large .idx files

The size of the index is determined by the number of bins, and in theory it should be optimizing itself for size, among other things. For what it's worth, 1.6MB can be the size of just the header, ...

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• Derek Caetano-Anolles
• February 24, 2020 17:57
• 1 vote

1. Community
2. Germline
3. unable to create contig_ploidy_model

Here is a description of how to use DetermineGermlineContigPloidy and GermlineCNVCaller to do the type of CNV analyses you are looking for. If you need more information, the DetermineGermlineContig...

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• Derek Caetano-Anolles
• February 24, 2020 15:00
• 2 votes

1. Community
2. Somatic
3. MergeBamAlignment Error: ArrayIndexOutOfBoundsException

This is most likely an issue related to formatting or mismatches in read length between files. In Java, the ArrayIndexOutOfBoundsException is usually outputted when an index is passed to an array t...

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• Derek Caetano-Anolles
• February 24, 2020 12:29
• 2 votes

1. Community
2. Germline
3. Missing PS field in the VCF file produced by GenotypeGVCFs

Using GenotypeGVCFs, it is normal behavior for a trailing field to be dropped if it is empty.So, if this is causing you issues downstream of your pipeline, a workaround would be to add a filler fie...

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• Derek Caetano-Anolles
• January 14, 2020 09:45
• 1 vote