User: S AR

gravatar for S AR
S AR50
Reputation:
50
Status:
Trusted
Location:
Pakistan
Last seen:
3 days, 6 hours ago
Joined:
3 years, 10 months ago
Email:
a*********@gmail.com

Posts by S AR

<prev • 58 results • page 1 of 6 • next >
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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 27 days 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 4 weeks 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 4 weeks ago by S AR50 • updated 4 weeks ago by Pierre Lindenbaum116k
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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 4 weeks 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 4 weeks ago by S AR50 • updated 4 weeks ago by Pierre Lindenbaum116k
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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 9 weeks 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 9 weeks 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 9 weeks ago by S AR50
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Comment: C: Getting unusual characters while generating output files in a bash script
... Yes there are first i'm trying to do this if i get success that i make a loop or something. And i ran : dos2unix ../pre_xdr_20_batch_run.sh It outputted: dos2unix: converting file ../pre_xdr_20_batch_run.sh to Unix format... But i found no change.. ...
written 9 weeks ago by S AR50
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6 follow
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Getting unusual characters while generating output files in a bash script
... Hi i im trying to run one command on mutliple files so i made a .sh script to do it: bwa mem -M -R '@RG\tID:ERR040140\tLB:2517707\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR040140' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR040140_* > ERR040140.sam bwa mem -M -R '@RG\tID:ERR046796\tLB ...
sh bash unix linux written 9 weeks ago by S AR50

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