User: giannkas1

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giannkas10
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Posts by giannkas1

<prev • 6 results • page 1 of 1 • next >
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Does anyone know how to get single-dose markers from VCF file containing variants from sugarcane?
... I have a huge VCF file with all variants genotyped from a population of 95 individuals. I have filtered just for biallelic SNPs but now I need the Single-Dose Markers (SDMs) in order to build a genetic map. According to definition of Wu et al. 1992, a SDM is considered as a single-allele copy from o ...
vcf single-dose markers genetic map written 8 months ago by giannkas10
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Comment: C: Best tool for variant calling in polyploids
... This one: https://github.com/ekg/freebayes I haven't tried it but I will. ...
written 11 months ago by giannkas10
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Comment: C: Best tool for variant calling
... Ok, I did it, thank you: https://www.biostars.org/p/403570/ ...
written 11 months ago by giannkas10
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Best tool for variant calling in polyploids
... To whom read this question, I hope this message finds you well. I am trying to build a genetic map for sugarcane and as I understand, one of the first steps is to call for variants. I have a sequenced (WGS data) bi-parental population of 95 sugarcane individuals (including both parents). I already ...
genome assembly snp written 11 months ago by giannkas10 • updated 11 months ago by harish300
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Comment: C: Best tool for variant calling
... Kevin, thank you for your complete response! I hope this message finds you well. I was wondering if you have experience in variant calling for polyploids? I have a sequenced (WGS data) bi-parental population of 95 sugarcane individuals (including both parents). I already aligned them (Bowtie2 and P ...
written 12 months ago by giannkas10
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What is the most recommended software to construct a genetic map with SNP markers for a sugarcane cultivar?
... I have to construct a genetic map for a sugarcane cultivar using SNP markers. I have a population of 93 individuals and sequencing data is WGS. Until now I have found these softwares: TetraploidSNPMap, SEG-Map, Lep-Map, CRI-MAP, MSTmap and JoinMap but I don't have experience on none of those. Which ...
wgs sugarcane bi-parental population written 17 months ago by giannkas10 • updated 17 months ago by h.mon31k

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