
Wondessen Ayalew
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Recent activity by Wondessen Ayalew Sort by recent activity-
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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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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Am I suppose to repeat the haplotype caller stage again?
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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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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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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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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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Dear David, Thank you for your kind replay. When I check the recalibrated bam file MT is avilable.
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Dear All, Thank you for your valuable comments. Your suggestions are working well regarding my GATK config. questions. In Addition, sorting of vcf file (dbSNPs) avoid the warning message posted in ...
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Dear GATK team, This is my first time running GATK and has faced a long time running GATK4.3 (> 17 hrs) and still not converge/finished. 1. Is there any solution to speed up the process? because I ...