
Chris Kachulis
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Activity overview
Latest activity by Chris Kachulis-
Chris Kachulis commented,
Hi Shashwat Sahay,Yes, you can use CrosscheckFIngerprints for panel data.The low LOD scores you are seeing generally imply that not very many of the fingerprinting sites are well covered. This cou...
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Chris Kachulis commented,
Hi Thomas Bradley, Once the number of unique read pairs, and total number of read pairs are found, the following equation is used:C/X = 1 - exp( -N/X )whereX = number of distinct molecules in lib...
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Chris Kachulis commented,
Jack Koskinen you can also use this 1000G vcf, from the same google bucket as the truncated version, instead.
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Chris Kachulis commented,
Hi Tiffany Kosch, The requirement of chromosomes being less than 2^31 bases is required for bams. The requirement of being less than 2^29 bases (around 512 million base pairs) is to be able to cre...
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Chris Kachulis commented,
Hi Elin Mehrasa,It looks like perhaps the question here is not completed? If you are still running into issues could you add some more details about the problem?
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Chris Kachulis commented,
Vishal Negi the PR I reference above was merged recently, so this should be fixed as of 4.4.0.0
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Chris Kachulis commented,
Hi LY Wang, You are right the the documentation here is a bit unclear, and seemingly contradictory. The solution is found in one of the comments on the other issue you linked to, here. With BQSR,...
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Chris Kachulis commented,
Hi Tanveer Ahmad,You can either lift your vcf over using LiftoverVcf, or reprocess your data using the T2T reference instead of hg38.
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Chris Kachulis commented,
Hi Adeline, One thing to note, Liftover only knows about the REF and ALT in the input (in your case hg19) and the REF in the output (in your case hg38) references. It does not know anything about ...
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Chris Kachulis commented,
This post may be helpful as well: https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Reference-genome-format