Closed x811zou closed 6 years ago
@x811zou Hi, did you find a way? I have a sample containing cells from different individual (singlecell RNA seq). I wonder if my vcf output run on the bam file while contain several genotypes or one hybride genotype? Thanks!
Not sure what you're talking about, but you need an external genotype data.
On Thu, Feb 21, 2019 at 1:06 PM HichamAffia notifications@github.com wrote:
@x811zou https://github.com/x811zou Hi, did you find a way? I have a sample containing cells from different individual (singlecell RNA seq). I wonder if my vcf output run on the bam file while contain several genotypes or one hybride genotype? Thanks!
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Thanks for the answer, my question is can I run the variant call on a bam file containing sequences from 3 individuals? Will the VCF file output have 3 different variant profile or one hybrid profile. Sorry if the question was confusing, hope it clarifies!
You need VCF file from SNP array (typical), or you could use VCF from sequence data, but focus on polymorphic sites in 1000G with MAF >1% or so focusing on exome regions to avoid false positives.
On Thu, Feb 21, 2019 at 2:29 PM HichamAffia notifications@github.com wrote:
Thanks for the answer, my question is can I run the variant call on a bam file containing sequences from 3 individuals? Will the VCF file output have 3 different variant profile or one hybrid profile. Sorry if the question was confusing, hope it clarifies!
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We may consider a SNP array in the future, but that would not be soon enough. If I could just ask for further clarification, what if my individuals are not in the 1000G. I should be able to build my own VCF from my sequencing data. I also have the BAMs for the the individual from sample that were not pooled and from which I could create differents VCF files. Can I feed demuxlet different vcf file or could I just merge them? Thanks!
Hello, I think I have this issue as well. I have a single 10x .bam file, which contains 5 multiplexed samples, and then five different .vcf files (one for each of the samples, generated through GATK from RNA-Seq data). Should we use something like GATK's CombineVariants to make these 5 files into 1 .vcf file? Or is there a different, preferred technique?
Yes you should merge them for demuxlet, I used monovar successfully, but that is for single cell, it’s a wrap that uses samtools.
Le 22 mars 2019 à 15:23, kmuench notifications@github.com a écrit :
Hello, I think I have this issue as well. I have a single 10x .bam file, which contains 5 multiplexed samples, and then five different .vcf files (one for each of the samples, generated through GATK from RNA-Seq data). Should we use something like GATK's CombineVariants to make these 5 files into 1 .vcf file? Or is there a different, preferred technique?
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Hello, I think I have this issue as well. I have a single 10x .bam file, which contains 5 multiplexed samples, and then five different .vcf files (one for each of the samples, generated through GATK from RNA-Seq data). Should we use something like GATK's CombineVariants to make these 5 files into 1 .vcf file? Or is there a different, preferred technique?
Hi, I have the same issue. Could I know how to generate different vcf files using the single merged bam file? Thank you!
Hi! In the demuxlet paper, I did not find the place commenting on how did you make the .vcf file for the 8 individuals. Could you specify it a bit? Thanks!