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Wiebe Kooistra

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Latest activity by Wiebe Kooistra
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    Wiebe Kooistra commented,

    Hey, Sure. Here is the VCF output line: SL4.0ch11 25548831 . T C,A 4.09785e+06 PASS AC=1,0;AF=0.523,0.006162;AN=2;BaseQRankSum=-0.295;DP=257674;ExcessHet=-0;FS=0;InbreedingCoeff=0.6408;MLEAC=819,8;...

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    Wiebe Kooistra commented,

    Hi Genevieve Brandt (she/her) I did read about the local realignment. There are 173 ArtificialHaplotypeRG's marked sequences. That the numbers don't add up I understand, I was just wondering why my...

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    Wiebe Kooistra created a post,

    ArtificialHaplotypeRG makes variant heterozygous

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    Dear GATK, Why do I see the Artificial Haplotype RG add more heterozygosity? In the top part we have the bam file after using HaplotypeCaller with the option --bamfile. In the lower part there is ...

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    Wiebe Kooistra commented,

    Hi Pamela Bretscher, I do not have a bamout image for this. The command that was run: gatk HaplotypeCaller -R ref.fasta -ERC GVCF --dont-use-soft-clipped-bases true --do-not-run-physical-phasing tr...

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    Wiebe Kooistra commented,

    Hey Pamela Bretscher The full GVCF line is: Ls_98839 100 . A <NON_REF> . . END=100 GT:DP:GQ:MIN_DP:PL 0/0:2007:0:2007:0,0,0 The stack trace is: 15:11:08.430 INFO NativeLibraryLoader - Loading libgk...

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    Wiebe Kooistra commented,

    Hey Pamela, For the GVCF file do you want to see multiple lines or just of the SNP location that I am expecting? For the full stack trace? Do you mean the output HaplotypeCaller is giving when runn...

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    Wiebe Kooistra commented,

    Hey Pamela Bretscher, I am using HaplotypeCaller and not Mutect2, but I did change --pruning-lod-threshold to the same levels as the gentlemen did (1.3, 0.5 and 0.1). The genotype and the GQ score ...

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    Wiebe Kooistra commented,

    Hi Pamela Bretscher, Thank you for you answer. I looked at all suggestions in both links. I found that if I turn off the downsampling, the GQ value becomes 0: Ls_98839 100 . A <NON_REF> . . END=100...

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    Wiebe Kooistra created a post,

    SNP VCF file and bamout not the same

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    Dear GATK, We are trying to retrieve a SNP that is present in the BAM file when using BWA-MEM. When looking at the bamout file we can see that there is a SNP (A->G), but when looking into the VCF f...