E Ra
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Activity overview
Latest activity by E Ra-
E Ra commented,
Hi Gökalp, I am not sure I understand what you meant by importing samples. I tried the codes below and I still do have no variants in the resulting vcf.gz file. My codes were: java -DGATK_STACKTRA...
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E Ra commented,
Hi Gökalp, I would like to try that. How would the code look like? Thank you
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E Ra commented,
Hi Gökalp, Here are two variant sites. Chr1A 15167 . G <NON_REF> . . END=15224 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,32Chr1A 15225 . C <NON_R...
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E Ra commented,
Hi Gökalp That helps. Thank you very much for the answer.
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E Ra commented,
Hi Gökalp, Below is the excerpt from a gvcfile bcftools view -H line1_BQSR_fromPass2_g.vcf.gz | head -n 4 Chr1A 1 . C <NON_REF> . . END=34 GT:DP:GQ:MIN_DP:PL ...
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E Ra commented,
Hi Gökalp After some research, I think that the fastq files of the lines of the same group need to be concatenated before the variant calling step. Thank you!
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E Ra created a post,
How to create a vcf file with variants of pooled lines?
Hello, How to create a vcf file that contains variants of two groups of lines (instead of variants per line)? A group is a pool of 5 lines. Lines 1-5 belong to the group 1; while line 6-10 belong t...
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E Ra commented,
Hi Gokalp, I used BWA aligner. My code was: parallel -j $(CPU} bwa mem -t 32 "${ref_fasta}" {}_R1.fq.gz {}_R2.fq.gz "|" samtools view -b -S -h ">" {}.orig.bam ::: $(ls -1 *_R1.fq.gz | sed 's/_R1.f...
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E Ra commented,
Hello, Sorry for the confusion. I just noticed that I could generate a BSQRplot01.pdf file for each sample. It is actually GATK BaseRecalibration report that contains graphs. My questions would rat...
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E Ra created a post,
GenotypeGVCFs generates empty vcf.gz files
Hello, I run GenomicsDBImport and then GenotypeGVCFs. As output files, I got vcf.gz files which have only header, and do not contain any variants. However, the variants are present in the input a...