User: siyavash_damdar

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New User
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20 hours ago
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9 months, 1 week ago
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s**************@yahoo.com

Posts by siyavash_damdar

<prev • 35 results • page 1 of 4 • next >
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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 4 months ago by siyavash_damdar20 • updated 4 months ago by Alex Reynolds26k
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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 4 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 5 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 5 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 5 months ago by siyavash_damdar20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... what are you thinking if I increase my memory an thread (RAM 64 and 16 thread)? ...
written 5 months ago by siyavash_damdar20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... so you mean my command is not a true way for all samples variant calling? java -Xmx16g -jar GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -R Equus_caballus.EquCab2.dna.toplevel.fa -T HaplotypeCaller -I sample-1.bam -I sample-2 -I sample-3 ......-I sample-60 -ERC GVCF -o output.vcf. ...
written 5 months ago by siyavash_damdar20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... thank you for your attention. I mean can I do variant calling for 60 samples or I should do it separately for each sample? because when I do it separately for each sample, I have only two Genotypes per SNP (0/1 or 1/1) in g.vcf files. ...
written 5 months ago by siyavash_damdar20
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variant calling for more than 60 samples using haplotype caller
... Hi I want to do variant calling for more than 60 samples using haplotype caller. I want to know, I should do it with multiple samples using this command : java -Xmx16g -jar GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -R Equus_caballus.EquCab2.dna.toplevel.fa -T HaplotypeCaller -I s ...
next-gen snp written 5 months ago by siyavash_damdar20
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Comment: C: mapping form different lane
... I want for SNP discovery. so if I want to map all files in one step then I faced problems in GATK? is it true? ...
written 5 months ago by siyavash_damdar20

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