User: sanjay.bpkihs

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Posts by sanjay.bpkihs

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SNP difference between isolates
... Hello, I have two .vcf files containing annotated SNP lists obtained from SNPeff for two different isolates of tubercle bacilli. I now wish to compare SNP differences between these two isolates. I wonder if there are any tools that I can use to perform the task. Thanks Sanjay ...
mycobacterium tuberculosis snpeff snp written 12 weeks ago by sanjay.bpkihs0 • updated 12 weeks ago by Medhat7.9k
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Comment: C: snpEFF chr not found error bacterial genome
... Hi, Thanks for your help. It finally worked. Just wondering what commands do you use to filter variants in vcftools? ...
written 5 months ago by sanjay.bpkihs0
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Comment: C: snpEFF chr not found error bacterial genome
... Hi, Thank you for your suggestions. I did align the file with Mycobacterium_tuberculosis_h37rv_gca_000277735 I changed the name to "Chromosome" and I double checked it to confirm. Then I ran with snpEff using the same command: java -Xmx4g -jar snpEff.jar Mycobacterium_tuberculosis_h37rv_gca_00027 ...
written 5 months ago by sanjay.bpkihs0
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SNPEff not showing SNP
... Hi I ran a command: java -Xmx4g -jar snpEff.jar Mycobacterium_tuberculosis_h37rv_gca_000277735 variants.vcf > R_variants.ann.vcf -v to annotate variants in vcf file that was produced using command: java -jar VarScan.v2.3.9.jar mpileup2cns mydata.mpileup --min-coverage 5 --min-var-freq ...
annotation forum snpeff variant snp written 5 months ago by sanjay.bpkihs0 • updated 3 months ago by cpad01129.3k
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Comment: C: snpEFF chr not found error bacterial genome
... Hi, I finally fixed the problem of ERROR_CHROMOSOME_NOT_FOUND. Thank you for the suggestion. But, the snpEff output shows SNP=0 INS=1508 Del=51 MIXED=6. However in varscan, for the same file, there were 1484 SNP and 75 Indels out of 1550 SNV's. I ran a command: java -Xmx4g -jar snpEff.jar Mycob ...
written 5 months ago by sanjay.bpkihs0
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Comment: C: snpEFF chr not found error bacterial genome
... Hi Can you help me more? How can i know CurrentName in my vcf file ? I am pretty new here. I will give one or two more try and then if i don't succeed i will send it to you. Thanks Sanjay Sanjay Gautam, B.Sc. MLT, M.Sc. Med. Microbiology PhD Scholar/School of Medicine/ Breathe Well Center Universit ...
written 5 months ago by sanjay.bpkihs0
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Answer: A: snpEFF chr not found error bacterial genome
... Hi ScienceBuff, Can you please guide me how can i change the naming of CHROM to Chromosome? I tried to follow http://snpeff.sourceforge.net/SnpEff_faq.html I used cat variant.vcf | grep -v "^#" | cut -f 1 | uniq to view the chromosome name and came up with "Chromosome Chromosomeosome" as an outpu ...
written 5 months ago by sanjay.bpkihs0
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Answer: A: snpEFF chr not found error bacterial genome
... Hi ScienceBuff, I hope you managed to solve your query regarding snpEff/MTB. I am having the same problem. Can you suggest me to solve this one?Thanks ...
written 5 months ago by sanjay.bpkihs0

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