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vctrymao

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  • MergeBamAlignment produces unknown error

    Answered

    I am using MergeBamAlignment:  ``` java -Dsamjdk.compression_level=5 -Xms3000m -Xmx3200m -jar /n/data1/hms/dbmi/park/alon/software/picard.jar \MergeBamAlignment \VALIDATION_STRINGENCY=SILENT \EXPEC...

  • Funcotator table format

    Is it possible to use Funcotator for germline calls but format the output in a table format instead of a VCF? I understand that MAF isn't yet available for germline Funcotator, but is there any oth...

  • Getting HaplotypeCaller SNP support in tumor

    I have a list of germline SNPs from HaplotypeCaller. I want to get the read level information, etc. of these SNPs in the tumor BAM file and format it into a VCF (ie. to see the read level support f...

  • HaplotypeCaller and low-VAF variants

    I am using HaplotypeCaller to generate germline variants. I noticed that HaplotypeCaller calls some variants with very low VAF values (see below):  What is the reasoning behind this? In what situa...

  • Missing mutations

    I am using the latest version of Mutect2 (4.1.9.0) and trying to call mutations from Mutect. I noticed that Mutect is not calling muations with clear read support in IGV. I tried some suggestions f...

  • Combining libraries for sample

    Answered

    I am trying to follow this guide in order to combine libraries for a single sample for alignment. However, the article seems to focus primarily on combining lanes. How should I combine multiple lib...

  • Using GenomicsDB with intervals

    Answered

    Hi, I am using GATK 4.1.2.0 and trying to run GenomicsDB with some gVCFs I have. I noticed that it requires an interval file; however, I am interested in running this across the whole genome, and t...

  • MarkDuplicates returns error with Multilane samples?

    I am using GATK 4.0.0.0. I am following this guide (https://gatk.broadinstitute.org/hc/en-us/articles/360035889471-How-should-I-pre-process-data-from-multiplexed-sequencing-and-multi-library-design...

  • Mutect tumor-only vs matched normal calls?

    Answered

    I am using GATK 4.1.2.0. This version includes the new FilterMutectCalls module.  I was wondering, is there anything different that Mutect2 does in tumor-only mode vs. in matched-normal mode? In th...

  • Germline mutations in Mutect2 vs HaplotypeCaller

    I am using GATK 4.1.2.0. I was wondering, is it usual to observe variants in the Mutect2 output that are labeled PASS but are still found by HaplotypeCaller? And is the reverse true: is it usual to...