
Leo
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Merge libraries before IndelRealignment
We have 4 libraries (4 paired-end fastq files) from the same sample. We did QC, alignment, MarkDuplicates separately. Should we merge the 4 libraries before IndelRealignment and BQSR? Will it make ...
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Whether Mutect2 discards alignments in variant calling
Hi, I am doing variant calling using Mutect2 tumor-only mode. Mutect2 seems to discard some alignment, probably because of quality. May I ask if Mutect2 will discard alignments? If so, what are the...
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Mutect2 tumor-only mode without normal match or germline resources
Hi, If I use Mutect2 in tumor-only mode to call somatic variants without any normal match, panel of normals (PON) or other germline resources. Will the results contain many germline variants? Will ...
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How number of somatic variants in the sample affects Mutect2 results?
Hi, I am calling somatic variants from an artificial cell mixture using Mutect2. The sample contains many more somatic variants than somatic mutation events in human tissue. Will Mutect2 (Calling, ...
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Defination of PF_ALIGNED_BASES and PF_INDEL_RATE
Hi, I am using Picard (2.9.0) CollectAlignmentSummaryMetrics. May I ask how PF_ALIGNED_BASES is counted? Does it include both match and mismatched bases and exclude all indels, gaps and soft/hard ...
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GenomicsDBImport: An index is required, but none found with file ending .idx
REQUIRED for all errors and issues: a) GATK version used: v4.4.0.0b) Exact command used: /gatk/gatk GenomicsDBImport --java-options "-Xmx160G -Xms160G" -R "${REF}" -L "${BED}" --merge-input-interv...