User: swatipuraanik

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Posts by swatipuraanik

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Comment: C: Filtering Homeologous SNPs
... Yes, the same article, thanks ...
written 3.0 years ago by swatipuraanik30
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Filtering Homeologous SNPs
... Hello, I read in a recently published article that 'Homeologous SNPs identified from each genotype were eliminated using VCFtools'. Can anyone shed some light on which filtering option in the VCF tools would do that? Thanks in advance. Regards Swati ...
vcf tools snp written 3.0 years ago by swatipuraanik30 • updated 3.0 years ago by harold.smith.tarheel4.4k
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Comment: C: vcftools does not filter by GQ
... Thank you for explaining this AP. I was troubled by the same situation. ...
written 3.2 years ago by swatipuraanik30
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GQ and DP filtering VCFtools
... `--minGQ ` & `--maxDP ` options require that the `GQ` and `DP` FORMAT tag is specified for all sites. Can you please clarify that if `./.` is present in any of columns in the format field, does it mean that `GQ` and `DP` are unspecified? ``` Sample 1 Sample 2 ...
vcftools snp written 3.2 years ago by swatipuraanik30 • updated 3.2 years ago by RamRS23k
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Comment: C: Qual score in VCF file
... As I was looking as a filtered.recoded VCF file, I went back & checked the raw VCF file as well. This file had all the values for QUAL & INFO field. My service provider have responsed as 'The TASSEL-GBS pipeline does not calculate quality scores for any sites, but assigns an arbitrary, unifo ...
written 3.2 years ago by swatipuraanik30
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Comment: C: Qual score in VCF file
... Thank you for the link & your suggestions. As implied there, the first one is a no-call site because there is no QUAL and no genotype, which holds true for the first SNP. Still confused about the second though! The VCF header says nothing specific about qual: ``` ##fileformat=VCFv4.0 ##Tas ...
written 3.2 years ago by swatipuraanik30 • updated 3.2 years ago by RamRS23k
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Comment: C: Qual score in VCF file
... Thanks for the thread. But in the example posted there, isn't the lowQual for specific for the 'Filter' column and not the 'Qual' column? In that case, if the variant will passes the filtering criteria/ threshold, the genotyper will insert a dot. If the variant fails the the filtering criteria/ th ...
written 3.2 years ago by swatipuraanik30
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Comment: C: Qual score in VCF file
... Thanks for your reply Ram,but I am sure of looking at the QUAL column. An example #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 10 ET_C6390828 41 S1_612208905 G T . PASS .;DP=119 GT:AD:DP:GQ:PL ./.:0,0:0 ./.:0,0:0 ET_C6410100 69 S1_614033230 A G . PASS .;DP=2833 GT:AD:DP:GQ:PL 0/1:19, ...
written 3.2 years ago by swatipuraanik30 • updated 3.2 years ago by genomax70k
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Qual score in VCF file
... Hello, As I understand, QUAL is a representation of accuracy of genotyping. But what does a '.' represent under the QUAL column in a VCF file? I do not have any numeric value for Phred-scaled score for assertion of ALT allele in the entire column. What does this mean for filtering low quality SNPs ...
vcf qual filtering written 3.2 years ago by swatipuraanik30 • updated 3.2 years ago by RamRS23k

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