Fastq Analysis For Loh Calls
I have Illumina sequencing files i.e fastq files. These are intended to generate Loss of heterozygosity (LOH) calls on analysis. Could you suggest a analysis pipeline/s which could be used for the purpose?
1 answer
A google search shows that VarScan does this but you'll have to align your reads first using a short-read aligner.
Also see this previous biostar question
Log in to answer this question.
More posts like this
-
How can I experimentally validate LOH?
written by deyugb2012 •
-
Generating Counts Data From Fastq Sequence Files
written by josph.sh •
-
Hiseq Analysis Software Alignment
written by Nicola Casiraghi
-
What Does A Dynamic Programming Table For An Hmm Look Like?
written by corn8bit •
-
Bwa Mem: How To Specify The Fastq Phred Format?
written by Giovanni M Dall'Olio
-
Convert Illumina 1.3 To Illumina 1.5
written by Giovanni M Dall'Olio
-
X-Seq: Can You Provide A Listing Of The Various Applications For Sequencing Technologies?
written by polarise
-
Pswms For Rna Binding Proteins
written by Anima Mundi
-
Loss Of Heterozygosity Calls On Snp Annotated File
written by Jane •
-
Export2Fastq Conversion
written by Biomed
