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Wondessen Ayalew

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Latest activity by Wondessen Ayalew
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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. VCF file SNP ID missing

    I used this "gatk VariantAnnotator -R reference.fasta -V input.vcf -O output.vcf --dbsnp dbSNP.vcf". Still, the problem is existing in my vcf file.

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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. VCF file SNP ID missing

    Could you please send me the full command and suggest me by what tool am I going to annotate it?  I am quite new for Bioinformatics. Thank you so much!

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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. VCF file SNP ID missing

    Am I suppose to repeat the haplotype caller stage again?

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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. VCF file SNP ID missing

    So what shall I do now? I do have 150 samples and it takes more than  6 month. Is there any way to solve at this stage?

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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. VCF file SNP ID missing

    Hello SkyWarrior, When I run BQSR, I used dbSNPs while during HaplotypeCaller I did not use --dbSNP option. Now, I use -D dbSNP when I try to combine individual VCF files and still the ID part is m...

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    Wondessen Ayalew created a post,

    VCF file SNP ID missing

    1. Community
    2. New User Advice

    REQUIRED for all errors and issues: a) GATK version used:  GATK 4.3.0b) Exact command used:  I used the command stated on gatk4.3.0 without any modifications and I  combine and genotyped my vcf fil...

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    Wondessen Ayalew commented,

    1. Community
    2. Documentation Questions
    3. Values for QD annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.

    Dear Dr, Genevieve Brandt, I got the same problem form GATK4.3.0. Based on your suggestion, I run "VariantRecalibrator model" and the problem still persists. Is there any other way to fix such prob...

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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. ApplyBQSR

    While i am running haplotypecaller, it took more than 6 days for one sample to generate g.vcf file. Menwhile, I am convinced to call only the MT variants and continue the nuclear variants later. Wo...

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    Wondessen Ayalew commented,

    1. Community
    2. New User Advice
    3. ApplyBQSR

    Dear David, Thank you for your kind replay. When I check the recalibrated bam file MT is avilable.

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    Wondessen Ayalew created a post,

    ApplyBQSR

    1. Community
    2. New User Advice

    REQUIRED for all errors and issues: a) GATK version used: GATK4.3  b) Exact command used: gatk ApplyBQSR -R ../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa -I ../data/mapped/ABigar/Abi1_dedup.ba...

    • Wondessen Ayalew
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    • 10 comments
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