User: jimkozubek

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jimkozubek20
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Posts by jimkozubek

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Multi-allelic CNV (Beginner's level question)
... Here is an example such that Copy Number is listed as 3|5|4|7 for only one sample and only one platform HISEQX. I have posed the question to MSSNG Sample Chromosome Start End CNVType CopyNumber Size Overlap Putative_Inheritance GC_Content_Percent CytobandAnn Gene_ ...
written 8 months ago by jimkozubek20 • updated 8 months ago by Kevin Blighe52k
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Comment: C: Multi-allelic CNV (Beginner's level question)
... Thank you. The HMM insight sounds correct. I am not sure these split values are due to various sequencing platforms, because in this case each line is a specific sample, and only one sequencing platform is identified per sample, such as each line says CG or HiSeqX, and only one per line. So, 3|4 ...
written 8 months ago by jimkozubek20
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Multi-allelic CNV (Beginner's level question)
... I am looking at some CNV information, which I did not run, but obtained from the MSSNG database. And after reading the documentation, I still have a question. The field CopyNumber sometimes lists values with just one number such as 0 or 3, but sometimes it looks biallelic, such as 3|4 or just 0|1 ...
cnv written 8 months ago by jimkozubek20 • updated 8 months ago by Kevin Blighe52k
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Comment: A: How to Turn Multiple ALT alleles to Genotype Calls
... Thanks for the pro tip! ...
written 17 months ago by jimkozubek20
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How to Turn Multiple ALT alleles to Genotype Calls
... I have a VCF file and many lines have multiple ALT alleles such as: 1 104159 . CA C,TA,TTT I have an algorithm that takes genotype data in a 0,1,2 matrix form. I am wondering if there are any standards or best practices in how to turn VCF lines with multiple ALT alleles (0/0, ...
genotype written 17 months ago by jimkozubek20
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Answer: A: Merging public vcf files: <NON_REF> in ALT
... I will answer my own question: I started with single sample VCF files and some had lines with 0/0 calls with alt designated by NON_REF "bcftools merge" created problems for me because it treated NON_REF as a literal ALT allele, which sometimes made other 0/1 calls turn into 0/2 calls. However, ...
written 17 months ago by jimkozubek20
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Merging public vcf files: <NON_REF> in ALT
... I am working with publicly available data sets of VCF files. I accessed VCF files broken out by patient and by chromosome with just the 0/0 calls, and unfortunately the ALT column includes a value on every line. I also have VCF files per patient with 1/1 and 0/1 calls across the entire genome, th ...
vcf gatk bcf written 17 months ago by jimkozubek20
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Comment: C: Can´T Find The Snps With Samtools (Only Get Indels)
... Pilar, I am having trouble with this same situation. I have a VCF file with only indels. Did you figure out why this occured? Jim ...
written 7.3 years ago by jimkozubek20

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