User: sanjay.bpkihs

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Posts by sanjay.bpkihs

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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 20 days 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 22 days 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 0.90 --p-va ...
annotation forum snpeff variant snp written 25 days ago by sanjay.bpkihs0
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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 25 days 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 25 days 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 25 days 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 28 days ago by sanjay.bpkihs0

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