User: prasundutta87

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prasundutta87170
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Posts by prasundutta87

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Comment: C: Strategy in WGS variant calling using GATK (CombineGVCF step)
... They are just warnings..Haplotypecaller did not find any reads in that position and hence genotype likelihhod could not be calculated. vdauwera can correct me here.. ...
written 18 days ago by prasundutta87170
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Comment: C: Strategy in WGS variant calling using GATK (CombineGVCF step)
... They are not error but warnings,, check this: https://gatkforums.broadinstitute.org/gatk/discussion/comment/42636#Comment_42636 ...
written 28 days ago by prasundutta87170
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Comment: C: Strategy in WGS variant calling using GATK (CombineGVCF step)
... Thanks a lot Geraldine. It does make sense. The whole selectvariants (splitting gvcfs) stage can be avoided then.. I split the GVCFs because I thought smaller gvcfs will make the job faster.. ...
written 4 weeks ago by prasundutta87170
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Comment: C: Strategy in WGS variant calling using GATK (CombineGVCF step)
... Yes..I did that only.. --native-pair-hmm-threads allows you to define no. of threads that will be utilised to compute the pairHMM step of haplotypecaller... For more information, check this: https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.3.0/org_broadinstitute_hellbender_tools ...
written 4 weeks ago by prasundutta87170
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Comment: C: Strategy in WGS variant calling using GATK (CombineGVCF step)
... I used the default: java -Xmx8g -jar HaplotypeCaller -R --native-pair-hmm-threads 4 -I -ERC GVCF -O output.g.vcf ...
written 4 weeks ago by prasundutta87170
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Comment: C: Strategy in WGS variant calling using GATK (CombineGVCF step)
... You are right. Water buffalo does not have a known sites VCF file. I have avoided this step. This document may help:https://software.broadinstitute.org/gatk/best-practices/workflow (especially **What is not GATK Best Practices?**) The main point here is you may report that you have 'adapted' the G ...
written 4 weeks ago by prasundutta87170
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Strategy in WGS variant calling using GATK (CombineGVCF step)
... Hello, It is a known fact that GATK does not scale or work very well when a draft assembly has a lot of contigs. Mine has 366989 (water buffalo reference genome). I have successfully generated GVCFs of all my 81 samples for the whole genome through Haplotypecaller without any errors. It usually fai ...
variant calling gatk snp wgs written 4 weeks ago by prasundutta87170
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Comment: C: addressing software versions
... Luckily I ran with default parameters and had not set -mbq..and I am running the gvcf generation per sample now..theoretically it should not change at all..but again..as genomax suggested..from a publication point of view, this change of version will be a difficult thing to sell..the reviewers will ...
written 3 months ago by prasundutta87170
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Comment: C: addressing software versions
... I agree with that..from a publication point of view, it definitely makes sense..I am just concerned over the time being wasted.. ...
written 3 months ago by prasundutta87170
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addressing software versions
... Hi, I started using GATK v4.0.0.0 on some of my WGS samples some days back. Few samples got a bug- "HaplotypeCaller exception: contig must be non-null and not equal to *, and start must be >= 1". I checked online and found that this bug was solved in the new sub-version. I downloaded GATK v4.0 ...
software error gatk best practices written 3 months ago by prasundutta87170

Latest awards to prasundutta87

Supporter 4 weeks ago, voted at least 25 times.
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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