Faezeh Darbaniyan
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Activity overview
Latest activity by Faezeh Darbaniyan-
Faezeh Darbaniyan commented,
In case that I redo gatk Haplotypecaller to get gvcf file, what is the best way to turn the combine.gvcf into vcf format?
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Faezeh Darbaniyan commented,
Thank you!
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Faezeh Darbaniyan commented,
Thanks again! Is there any way to combine vcf files in gatk? Do I have to repeat the previous step (HaplotypeCaller) and create gvcf file?
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Faezeh Darbaniyan commented,
Hello, Thank you so much for your quick reply! They are not gvcf. In fact they are in form of vcf. Does it cause an issue?
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Faezeh Darbaniyan created a post,
gatk CombineGVCFs output contains only one Chr
REQUIRED for all errors and issues: a) GATK version used: gatk4/4.4.0.0 b) Exact command used: gatk CombineGVCFs \ -R ${gencode_path}/hg38.fa \ -V ${data_output}/15650_raw_variants.vcf \...
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Faezeh Darbaniyan commented,
Thank you so much! You are right and I had a typo in my code. Now it works perfectly and I got my results. Appreciate! Faezeh
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Faezeh Darbaniyan commented,
And here is for ApplyBQSR: 23:36:27.258 INFO ApplyBQSR - ------------------------------------------------------------ 23:36:27.260 INFO ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.4.0.0 23:...
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Faezeh Darbaniyan commented,
Thanks for explaining. Here is the top lines of BaseRecalibrator: 23:23:43.288 INFO BaseRecalibrator - ------------------------------------------------------------ 23:23:43.290 INFO BaseRecalibra...
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Faezeh Darbaniyan commented,
To me it looks like issue is happening at ApplyBQSR step. Am I right? Here is the fastqc of raw fastq files (R1 & R2), Filename sample1_R2.fastq.gz File type Conventional base calls Encoding...
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Faezeh Darbaniyan commented,
Hi, Do you mean this log (I had provided it in previous comments)? gatk BaseRecalibrator \ -I ${aligned_reads}/sample1_sorted_dedup_reads.bam -R \ ${gencode_path}/hg38.fa \ ...