User: rastogi.suraj93

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Posts by rastogi.suraj93

<prev • 18 results • page 1 of 2 • next >
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Comment: C: problem in annotate my vcf file with another vcf file ??
... sorry, i used but i forgot to mention there .. ...
written 3.1 years ago by rastogi.suraj9330
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Comment: C: problem in annotate my vcf file with another vcf file ??
... sorry, I again edit my question...please check it ...
written 3.1 years ago by rastogi.suraj9330
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problem in annotate my vcf file with another vcf file ??
... hello every one, I am trying to annotate my vcf files which is generate using same reference genome for both vcf files but query reads is different. after alignment and SNP calling i got vcf file and count also variants. now i want to annotate these files to each other. i am using vcf annotate comma ...
genome next-gen snp written 3.1 years ago by rastogi.suraj9330 • updated 2.9 years ago by Biostar ♦♦ 20
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compare two vcf files which generate using bcftools
... hello every one, i am trying to compare two vcf files generate by using bcf tools and i am use this command for compare and find comman snp position between in these two files- **vcf-isec -n +2 input_1.vcf input_2.vcf | bgzip -c > output.vcf.gz** but i am getting error .. i would like to appre ...
vcf samtools alignment analysis snp written 3.1 years ago by rastogi.suraj9330
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Comment: C: keep the variants ID after filteration
... Ok, thank you so much. I will try like this. ...
written 3.2 years ago by rastogi.suraj9330
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Comment: C: keep the variants ID after filteration
... yeah, in my snp file have chr position but SNP ID is not mention. at the column of ID is mention only 0. I want also give SNP ID in my file like rs58108140 rs71262674 rs71262673 so how can I give to SNP ID in my vcf file? ...
written 3.2 years ago by rastogi.suraj9330
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Comment: C: keep the variants ID after filteration
... No I dont have. I have vcf file without SNP ID like - #CHROM POS ID REF ALT QUAL NC_00839 536376 0 TAGCTAGCT TAGCTAGCTAAGCTAGCT 96.5 ...
written 3.2 years ago by rastogi.suraj9330
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Comment: C: keep the variants ID after filteration
... yeah..so please suggest me any other tools and command ...
written 3.2 years ago by rastogi.suraj9330
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keep the variants ID after filteration
... Hello everyone, I would like to appreciate if some one help me. I tried to make SNPs ID in VCF file REplace to 0 but facing some problem which occur by commands. my commands is /SnpEff cat variants.vcf | java -jar SnpSift.jar filter --set my_rs.txt "ID in SET[0]" > filtered.vcf and after getti ...
alignment next-gen sequence snp written 3.2 years ago by rastogi.suraj9330 • updated 3.2 years ago by dschika290
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(Closed) SNP annotation for variants validation.
... Hi every one, I appreciate if some one help me to solve my problem. my problem regarding SNP validation. I have a SNP data in vcf file format and I already download the db SNP data set for SNP annotation for validation. this file is in BED file format. can any one suggest me work flow of SNP validat ...
next-gen chip-seq snp written 3.2 years ago by rastogi.suraj9330

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