David Moline
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Activity overview
Latest activity by David Moline-
David Moline commented,
Hi Gökalp Çelik, How do these look? chr13_32336895 chr13_32337144 chr13_32337995 chr13_32340733
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David Moline commented,
Hi Gökalp Çelik, Thank you for the in-depth response! I took some screenshots in IGV for each of the 4 samples. Under View > Preferences > Alignments > Show soft-clipped bases I enables soft-clippe...
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David Moline commented,
Here is the Mutect2 output (no annotation) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLEchr13 32336895 . G GTCTGTTTCATGAAGTTCCTTAGTATTTCCTAAAGCAAGATTAT...
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David Moline commented,
Hi Gökalp Çelik, This is WES of a tumor sample. Let me know if you need more info! Thanks, David
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David Moline created a post,
Mutect2 Variant has very long ALT allele
REQUIRED for all errors and issues: a) GATK version used: 4.4.0.0b) Exact command used: I am running Mutect2 using the workflow nf-core/sarek. The main script and config file are found on github (l...
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David Moline commented,
Hi Gökalp Çelik, So the results from GetPileupSummaries and CalculateContamination imply loss of heterozygosity potentially from copy number variation. Is there a way to visualize the copy number v...
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David Moline commented,
Hello Gökalp Çelik Here are the results using FilterMutectCalls. I also ran the data using LearnReadOrientationModel, GetPileupSummaries, and Calculate Contamination. This script should be very clo...
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David Moline commented,
Hello Gökalp Çelik, Here is a new screenshot using mutect2 via command line. The command I used is shown below (this basic script was repeated for each sample): gatk Mutect2 \--input /home/.../Mol...
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David Moline commented,
Here is a more readable screenshot:
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David Moline commented,
Gökalp Çelik Thank you for responding! Here are the mutect2 VCF outputs for each of the three variants. I do want to note that this observation (variant calling discrepancy) is not exclusive to jus...