User: princy149

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princy14960
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Posts by princy149

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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi, do you want to make LD for your snps data? I didn’t understand your question clearly but if you want to make LD for your data via TASSELS then choose chromosomes filter using its start site position and end site position which may be shown in your TASSELS, choose data for individual chromosomes ...
written 3 months ago by princy14960
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Comment: C: Compute Phylogenetic Trees Using Snps Data (VCF files)
... hi, i did it by myself in my project so have no idea about you tube but i want to tell you something of using TASSEL 4.3 and TASSEL 5, in case of 4.3 version you do not have to need convert your vcf data into sort-genotype file but if you will use TASSEL 5 then it need to first convert your vcf d ...
written 3 months ago by princy14960
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Answer: A: Compute Phylogenetic Trees Using Snps Data (VCF files)
... read its manual first and if you have problem then let me know..i will explain you steps.. ...
written 3 months ago by princy14960
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Answer: A: Compute Phylogenetic Trees Using Snps Data (VCF files)
... http://www.maizegenetics.net/tassel ...
written 3 months ago by princy14960
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Answer: A: Compute Phylogenetic Trees Using Snps Data (VCF files)
... Hi J J, If you want to create SNPs phylogenetic tree via Vcf files , then you can try “TASSELS” tool through which you can get more clear images of phylogeny tree. ...
written 3 months ago by princy14960
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(Closed) R program for comparing of two vcf files using their genomic position (chromosome: base pair position) and REF/ALT info and generating the percentage of match/ mismatch in output report .
... R program for comparing of two vcf files using their genomic position (chromosome: base pair position) and REF/ALT info and generating the percentage of match/ mismatch in output report . ...
R written 3 months ago by princy14960
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Comment: C: filling of missing genotype information in merged variant call vcf file
... Thank you so much Kevin, you'r really very helpful. I appreciate you very much for your hard work to making solution of my problem. I will sure Try This. Thank you again :) ...
written 3 months ago by princy14960
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Comment: C: filling of missing genotype information in merged variant call vcf file
... Thank you very much kevin for your reply. I will appreciate you for helping me and giving your precious time for this query. looking forward for your solutions for this. ...
written 3 months ago by princy14960
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Comment: A: filling of missing genotype information in merged variant call vcf file
... Thank you kevin for your prompt reply. I want to use individual gVCF files instead of Bam files for filling of GT info where it is not found. And also want to use Perl instead of java. This is a condition for me. ...
written 3 months ago by princy14960
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Comment: A: filling of missing genotype information in merged variant call vcf file
... This is "gVCF " format of one sampple, contains variant and non variant both sits. Chr01 229 . G <*> 0 . DP=91;I16=48,43,0,0,3625,145089,0,0,3283,119371,0,0,1834,42368,0,0;QS=1,0;MQSB=0.894166;MQ0F=0 PL:AD 0,255,255:91,0 Chr01 230 . T <*> 0 . DP=93;I16=47,44,0,0,3399,129511,0,0, ...
written 3 months ago by princy14960 • updated 3 months ago by Kevin Blighe28k

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