User: siyavash_damdar

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Posts by siyavash_damdar

<prev • 40 results • page 1 of 4 • next >
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The pooled heterozygosity (Hp) score
... Hello, I am working on a signature of selection study. I want to know, is there a software In order to calculate the pooled heterozygosity (Hp) score using a sliding window approach (100 kb with a step size of 50 kb)? My SNP data format is variant call format (VCF). Thanks ...
vcf genome next-gen snp gene written 3 months ago by siyavash_damdar20
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Comment: C: Extracting sample ID and their genotypes
... Dear finswimmer, In this data first column is included samples (A,B,C,etc), the second column is included genotypes (each number per SNP). So, I need to know, for example, how can I extract A B C samples and their genotypes together (all data in A B C rows) in a text file. ...
written 10 months ago by siyavash_damdar20
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Comment: C: Extracting sample ID and their genotypes
... No, my data format is not VCF. ...
written 10 months ago by siyavash_damdar20
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Comment: C: Extracting sample ID and their genotypes
... Dear finswimmer, Actually, it is a small example and my real data is much bigger than this dataset. The format is text (txt). Here the first column is included the individuals and the second column is their genotypes. I want extract the"A","B" and "C" genotypes in text file like this: A 1111212 ...
written 10 months ago by siyavash_damdar20
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Extracting sample ID and their genotypes
... How can extract these individuals "A", "B", "C" and their genotypes in this dataset? Is there a command in linux for this? A 11112121112121121102111121110 B 11211112112110211111211121110 C 20222222202020220202222222220 D 11111112112110211111211121110 E 20222222202020220202222222 ...
next-gen chip-seq snp written 10 months ago by siyavash_damdar20 • updated 10 months ago by paolo002150
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Gene symbol list
... Hi, I have many coordinates (approximatly1000), I want to know how can I find the gene symbols that are in these coordinates? Thanks, Siavash ...
sequence next-gen chip-seq snp written 15 months ago by siyavash_damdar20 • updated 15 months ago by Alex Reynolds28k
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expected heterozygosity calculation
... Hi to all, I have a vcf file that including multisample. I want to calculate expected heterozygosity for this vcf file by sliding-window approach(40-kb-windows slidingin20-kb-steps). I want to know, which software do this? Thanks, Siavash ...
vcf genome snp written 16 months ago by siyavash_damdar20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... Hi Thank you for useful comment. Yes of course, I did it. The best, Siavash ...
written 16 months ago by siyavash_damdar20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... sorry if bother you. Thanks ...
written 17 months ago by siyavash_damdar20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... so, according to your comments, I can have 3 scenarios: 1. call sample by sample and joint genotype 2.call all samples per region 3. call all samples (all regions) using multithreading so, Are there any differences in the results (genotypes) of these scenarios? ...
written 17 months ago by siyavash_damdar20

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Popular Question 5 months ago, created a question with more than 1,000 views. For SNP,INDEL counting per chromosomes in vcf
Popular Question 8 months ago, created a question with more than 1,000 views. For SNP,INDEL counting per chromosomes in vcf

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