User: S AR

gravatar for S AR
S AR50
Reputation:
50
Status:
Trusted
Location:
Pakistan
Last seen:
2 months ago
Joined:
4 years, 12 months ago
Email:
a*********@gmail.com

Posts by S AR

<prev • 60 results • page 1 of 6 • next >
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Comment: C: Making pattern of GT:AD:DP:PL column values to be replaced by o and 1.
... i tried gsub from R but it didnt work. As well i tried: ex -s -c '%1:1,.*/1/g|x' file.vcf ...
written 9 weeks ago by S AR50
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Making pattern of GT:AD:DP:PL column values to be replaced by o and 1.
... Im trying to replace GT:AD:DP:GQ:PL values from all samples in a multi vcf file with 1. My file looks like this: Pos 6620 6734 6737 6742 6750 7151 7212 7362 Alt A A A G GC A T G ERR038741 0 1:1,213:214:99:7391,0 0 0 0 0 1:2,205:207:99:7078,0 1:0,191:191:99:7383,0 ERR040140 0 1:1,33 ...
vcf python grep machinelearning linux written 9 weeks ago by S AR50 • updated 8 weeks ago by Kevin Blighe56k
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Annotating Mycobacterium tuberculosis VCF file using snpEFF and aNNOVAR
... Hi, I generated my vcf files from GATK pipeline using ploidy 1 as it is a mycobacterium tuberculosis genome. Now i want to annotate my variants using snpEFF and Annovar. I search snpEff database for mtb annotation using: java -jar snpEff.jar download -v Mycobacterium_tuberculosis it gave me ...
annotation snpeff mtb snp annovar written 14 months ago by S AR50
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Comment: C: How to combine a multi sample VCF from multiple sample VCF and interpret a multi
... command not working! ...
written 14 months ago by S AR50
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How to combine a multi sample VCF from multiple sample VCF and interpret a multi sample vcf of bacterial genome?
... I used GATK HaplotypeCaller for Variant calling of 2300 MTB strains. Now i want to make it a multi Sample VCF. I used CombineVariants but im comfuse that either this is correct or not. Each of my VCF is isolated means 1 VCF from one individual sample. But GATK says: CombineVariants can be used for ...
vcf gatk variant calling written 14 months ago by S AR50 • updated 14 months ago by Pierre Lindenbaum127k
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Comment: C: How to merge/combine multiple vcf from different samples to make one multi sampl
... Thank you it worked. ...
written 14 months ago by S AR50
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How to merge/combine multiple vcf from different samples to make one multi sample vcf file using GATK
... I have 2300 vcf files from 2300 samples generated from haplotypeCaller of GATK from bacteria. Now i want to combine all VCF into one as multivcf sample file. I used CombineVariants from GATK but it is giving error when i give -V *.vcf.gz. I cant write -V file name 2300 times can anybody help me with ...
gatk loop scripting written 14 months ago by S AR50 • updated 14 months ago by Pierre Lindenbaum127k
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Answer: A: Getting unusual characters while generating output files in a bash script
... The error was resolved using : #dos2unix sed `echo "s/\r//"` ../pre_xdr_20_batch_run.sh > pre_xdr_20_batch_run.sh Secondly I found an answer to run it in a loop : https://bioinformatics.stackexchange.com/questions/5635/how-to-run-same-command-on-multiple-files/5640?noredirect=1#comment ...
written 15 months ago by S AR50
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Comment: C: Getting unusual characters while generating output files in a bash script
... The only thing that change in the read group header will be tID and tSM. that will be the file names. ...
written 16 months ago by S AR50
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Comment: C: Getting unusual characters while generating output files in a bash script
... And if anyone suggest a better way of doing it like a loop that can get file name from a list? ...
written 16 months ago by S AR50

Latest awards to S AR

Popular Question 3 months ago, created a question with more than 1,000 views. For Splitting VCF file to decrease file size to run it on VEP and wANNOVAR
Popular Question 4 months ago, created a question with more than 1,000 views. For Splitting VCF file to decrease file size to run it on VEP and wANNOVAR
Popular Question 4 months ago, created a question with more than 1,000 views. For TypeError: 'str' object is not callable
Popular Question 13 months ago, created a question with more than 1,000 views. For SRA files bulk downloads
Popular Question 13 months ago, created a question with more than 1,000 views. For TypeError: 'str' object is not callable
Supporter 17 months ago, voted at least 25 times.

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