User: shrutishreyajha

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Posts by shrutishreyajha

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Comment: C: Convert vcf files with phased genotypes to standard haplotype format
... Hi, I am encountering the same problem with my VCF files and hap files creation with Ancestral/Derived Allele. I need that for running rehh package. Was your problem solved? ...
written 21 months ago by shrutishreyajha0
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Error while running R package rehh
... Hi I am working with 1000 Genomes Phase 3 data VCF files( *Completely Phased and Genotyped*). I want to Calculate EHH and IHH scores for this data for which I am using REHH 2.0 package of R. I filtered the VCF files using VCFtools, SNPs_only option, Extracted haplotypes from VCF file containing ...
R rehh snp written 21 months ago by shrutishreyajha0
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Comment: C: ERROR: Duplicate row.names not allowed
... Hi. Thanks a ton. How can I check that? ...
written 2.0 years ago by shrutishreyajha0
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Comment: C: ERROR: Duplicate row.names not allowed
... Hi Thanks for replying Can you tell me How to count and compare the number of row names and unique row names? ...
written 2.0 years ago by shrutishreyajha0
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ERROR: Duplicate row.names not allowed
... I am working with Rehh package of R . data2haplohh is a function within rehh. So my command goes like this: > chr2<-data2haplohh(hap_file= 'SNPs_only.chr2.impute.hap' , > map_file='chr2mapf1.inp', recode.allele= TRUE) The error I get is: " Error in read.table(map_file, row.names = 1 ...
R rehh written 2.0 years ago by shrutishreyajha0 • updated 19 months ago by Biostar ♦♦ 20
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Comment: C: Variant calling results in polyploidy data
... Hi I am getting the same error of "Error: Polyploidy found, and not supported by vcftools "6:6292579" The output of > grep -v "^#" chr6.vcf | cut -f 10- | cut -d ':' -f 1 |sort | uniq is giving : ***" 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 ...
written 2.1 years ago by shrutishreyajha0
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Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
... Hi I am trying to add ancestral allele to 1000 Genomes Phase3 VCF files. I have used the "human_ancestor_GRCh37_e59.tar.bz2" files for ancestral allele input file. The steps I have used are: > cat human_ancestor_3.fa | sed 's,^>.*,>1,' | bgzip -c > human_ancestor_3.fa.bz > samtoo ...
1000genomes tabix faidx samtools vcftools written 2.1 years ago by shrutishreyajha0

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