AMN
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Activity overview
Latest activity by AMN-
AMN commented,
That's quite helpful, thanks! I am still concerned about cases like the one I mentioned, but it is good to know that overall this gave you the best results.
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AMN created a post,
`FilterMutectCalls` for normal only calls
AnsweredWhy do I see that the guide for `CreateSomaticPanelOfNormals` is `FilterMutectCalls` not used after calling germline `Mutect2` variants? Is this just a suggestion, and how strong is that suggestion...
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AMN created a post,
producing strandedness metrics from rnaseq data
AnsweredI have what i believe to be unstranded RNA data, and when I ran CollectRnaseqMetrics with STRAND=NONE I got absolutely no strandedness metrics, which I would need to confirm that my sample is indee...
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AMN commented,
Hi Genevieve, We are still looking into the differences. However a preliminary look at the first few lines shows some differences already. The 42nd and 43rd line of the bam: spark-enabled: $ samto...
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AMN created a post,
ApplyBQSRSpark ApplyBQSR has different results
I am seeing a different result when i use ApplyBQSR vs ApplyBQSRSpark, using the exact same inputs. I tried with both GATK 4.1.0.0 and 4.1.9.0 i am comparing the command: gatk ApplyBQSR --java...
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AMN commented,
Sure, I took a single bam and produced two sorted bams with SortSam, one queryname-sorted and the other coordinate-sorted. I ran MarkDuplicates on each one the same way except for the `--ASSUME_SOR...
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AMN commented,
Hi Genevieve, Thanks for your reply. I tried MarkDuplicatesSpark and the results seem to match ReadsPipelineSpark rather than our implementation of MarkDuplicates. sample totalreads_MarkDuplicate...
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AMN commented,
Hi Genevieve, Thank you for your reply. I have generated a small table comparing the results of each (one using GATK 4.1.9.0 MarkDuplicates, the other using GATK 4.1.9.0 ReadsPipelineSpark). here'...
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AMN created a post,
Comparison between ReadsPipelineSpark and MarkDuplicates
GATK version: 4.1.0.0 and 4.1.9.0Comparing two processes:``` gatk MarkDuplicates \ --TMP_DIR ./ \ --MAX_RECORDS_IN_RAM 50000 \ --INPUT ${inputBam} \ --METRICS_FILE ${idSampl...
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AMN commented,
I am finding that MarkDuplicates and this tool ReadsPipelineSpark mark a different number of reads as duplicate (flag > 1024). Same version of gatk (4.1.0.0). Why is this the case? any configuratio...