User: ShahiRB

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ShahiRB0
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Posts by ShahiRB

<prev • 13 results • page 1 of 2 • next >
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Answer: A: bcftools FORMAT/FOO annotation to specific sample in multiple sample VCF
... Developer/s told me [(https://github.com/samtools/bcftools/issues/998)][1] that the bug mentioned above is fixed in the latest version. [1]: https://github.com/samtools/bcftools/issues/998 ...
written 9 months ago by ShahiRB0
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Request for EnsDb (.Hsapiens.v95) download link
... Hi guys, Can anyone pass me an URL for downloading **EnsDb(.Hsapiens.v95)**, if they have built already? Thanx! ...
rna-seq written 9 months ago by ShahiRB0 • updated 9 months ago by jared.andrews074.3k
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Comment: C: bcftools FORMAT/FOO annotation to specific sample in multiple sample VCF
... Hi @Pierre Lindenbaum, I think these steps [A-E] will help to illustrate more. (**SAMPLE2** that has to be annotated with "**FooValue1**" and "**FooValue2**", see in bold) **A]**. zcat annots.tsv.gz 1 752567 752567 FooValue1 12345 1 752722 752722 FooValue2 67890 **B].** zcat ...
written 9 months ago by ShahiRB0 • updated 9 months ago by finswimmer13k
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bcftools FORMAT/FOO annotation to specific sample in multiple sample VCF
... Hi, I wonder what do we have to modify in this command "bcftools annotate -a annots.tsv.gz -h annots.hdr -c CHROM,FROM,TO,FMT/FOO,BAR in.vcf" if we want to annotate FMT/FOO to SAMPLE2 (let's say the in.vcf has two samples) but not to SAMPLE1. I did like this "bcftools annotate -s SAMPLE2 -a annots ...
next-gen written 9 months ago by ShahiRB0
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Comment: C: Can anyone help me with normal-only calling for panel of normals(PON) with MuTec
... @Dan,hanx for your effort. I will update you with some tweaks from Geraldine_VdAuwera (GATK). Cheers! ...
written 4.0 years ago by ShahiRB0 • updated 5 weeks ago by RamRS25k
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Comment: C: Can anyone help me with normal-only calling for panel of normals(PON) with MuTec
... @Dan, I tried without XX:+AggressiveOpts argument; still the same problem. But the HaplotypeCaller runs perfect with the same bam and intervals list. ...
written 4.0 years ago by ShahiRB0
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Comment: C: Can anyone help me with normal-only calling for panel of normals(PON) with MuTec
... Hi Dan, 1. Even without passing intervals list I got the same results i.e no error, no variants in vcf, header only. 2. The bam file is perfect. Any further suggestions? Regards, ...
written 4.1 years ago by ShahiRB0 • updated 5 weeks ago by RamRS25k
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(Closed) anyone using MuTect2
... can anyone pass me the code for normal-only calling for panel of normals creation with MuTect2? Note: The code in the MuTect2 documentation does not work (ie the code does not spit any error as well as variants in vcf, except vcf header) ...
software error next-gen sequencing written 4.1 years ago by ShahiRB0
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Answer: A: Can anyone help me with normal-only calling for panel of normals(PON) with MuTec
... Thanx igor, but that doc abt mutect2 looks misleading . Actually HC does not have that argument. ...
written 4.1 years ago by ShahiRB0
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Can anyone help me with normal-only calling for panel of normals(PON) with MuTect2.
... Can anyone help me with normal-only calling for panel of normals with MuTect2. The code below does not spit any error as well as variants in vcf, except vcf header. Here is the code: java -Xmx45g -XX:+AggressiveOpts -jar /nexus/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar \ -T MuTect2 \ -R /home/ngs ...
software error next-gen written 4.1 years ago by ShahiRB0 • updated 3.8 years ago by 2nelly170

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