User: deepak.k.choubey

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Posts by deepak.k.choubey

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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! I will figure this issue out and get back. ...
written 9 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! I have an update! To my surprise, when I deleted that line 242 and ran bcftools normalization, it still gives the same error, now for the line 243: [E:vcf_parse_format] Format column with no sample columns starting at 1:13273 line 243: 1 13273 . G C 759 LowQual CSQ=C|downst ...
written 10 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! So, yes this line is the problem sine it has missing info. Regarding the generation of the merged VCF; which includes about 10000 samples, I know that the merged VCF files were created using GATK as the header of the merged VCF file state that. I have access only to the merged files so ...
written 10 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! No, there is nothing after "GT:AD:DP:GQ:PL" for this line; however, for the next line 243 there is "GD:AD:DP:GQ:PL:SDP:RD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR". So the genotype of this 242 line is missing I think? And, that is what causing the issue or please let me know if the matter cou ...
written 11 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! I used bcftools and performed normalization, but got this error below: [E:vcf_parse_format] Format column with no sample columns starting at 1:13244 In VCF: line 242: 1 13244 . G A 95 . CSQ=A|downstream_gene_variant|..............buch of info..... GT:AD:D ...
written 11 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! I will work on this and let you know. ...
written 12 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! Could you tell me what the normalization step will do here? Is it related to distribution of the mutations? And, by reading the normalized bcf to plink, do you mean this?: plink --bcf MyVariants.norm.bcf --make-bed --out XX Hence, instead of reading vcf files plink reads normalize ...
written 12 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks Kevin! I did that but don't know what the issue is as the 242nd line in VCF looks same like 243 line, one notable thing is that the line 242 is the very next line to the header "CHROM POS ID REF ALT ......". I cant paste the line here due to confidentiality etc.. It looks like this: In V ...
written 12 days ago by deepak.k.choubey50
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Comment: C: Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
... Thanks much Kevin! I uncompressed the vcf file and ran plink again. There was compression error and now it's solved, so I was able to run plink using the command: plink --vcf XX.vcf --make-bed --out XX The program ran well, however, gave an error : "line 242 of vcf file has fewer token than expec ...
written 12 days ago by deepak.k.choubey50
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Comment: C: GWAS analysis on merge TCGA exome data (vcf files)
... Thanks Kevin! Great Help! I now understand the concept. I have bioinformatics skills but am new to these type of GWAS analysis. I need to know what data I need to extract from the VCF file to plot these plots. To start with "Figure 4", practically speaking, to calculate the "number of SNPs/mutations ...
written 13 days ago by deepak.k.choubey50

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