Amit
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Activity overview
Latest activity by Amit-
Amit commented,
I was going through the documentation of GATK LeftAlignAndTrimVariants. It would be nice for GATK HaplotypeCaller to have options like --split-multi-allelics and --dont-trim-alleles if possible in ...
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Amit commented,
Certainly don't want the INFO and FORMAT fields getting messed up! Thank you for sharing your experience. I will take a look at these tools.
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Amit created a post,
Potential updates to GATK HaplotypeCaller documentation
In the HaplotypeCaller documentation, details for using --annotation/ -A option doesn't provide links/details for annotations like StrandBiasBySample, DepthPerSampleHC, AS_InbreedingCoeff, etc that...
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Amit created a post,
Reporting of multiple alleles at same genomic location as a separate record
How do I get GATK haplotypecaller to report multiple alleles at same genomic location as multiple records in VCF (one record for each allele) as opposed to a single record listing all alleles which...
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Amit commented,
The data sources are on central location that all nodes are trying to access. I will check with HPC team again. Thank you!
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Amit commented,
Hi Bhanu, Here is a quick update. Can you please run with stacktrace enabled and share the log with us? - Log stays the same and the process times out! Look forward to your thoughts.
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Amit commented,
Hi Bhanu. Please see my comments below in italic. The log file shared above, is that the entire log? if not please share the entire log file. - That is the entire log. The analysis ge...
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Amit commented,
Hi Bhanu, Sorry about the confusion due to incorrect reference information in my command. This command is run within a snakemake workflow where the values for options (-R, --data-sources-path and -...
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Amit commented,
Hi GATK Development Team, When do you think I can expect to hear from you on my query? Amit
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Amit commented,
Hi Bhanu, Gentle reminder. Could you please reply to my above query. Let me know if you need more information. Amit