gemBS aligner file format

Hello Everybody

Recently I got few files of WGBS data, which is aligned using gemBS. I have a question

How (Non-converted base count + Converted base count) is not giving the value of Total base. Does it mean that those extra values are for non CpG

This is my gemBS aligned file (header added)

Chr     Start   End    Ref call Genotype call   Methylation estimate    Non-converted base count    Converted base count    Total bases supporting genotype call    Total bases
chr1    10668   10669   G   G   1   3   0   6   6
chr1    10671   10672   G   G   1   4   0   7   7
chr1    10674   10675   G   G   1   5   0   10  10
chr1    10680   10681   G   G   1   7   0   12  12

Anybody, please comment on this

Regards Shrinka

gembs aligner

• 1,130 views • link

updated 5.3 years ago by GenoMax

• written 5.3 years ago by shrinka.genetics •

gemBS output files are described here. See if that helps.

• 0 views • link

written 5.3 years ago by GenoMax

0 answers

No answers yet.

More posts like this

Alignments on IGV display not matched to the result from "samtools mpileup"
written 4.2 years ago by magicRG •

I had two .bam files from the same reference genome sequences. When I used the command of "samtools mpileup " to find SNPs/InDels. The command …
Compare genotype genome sequences at basepair level
written 4.8 years ago by kashiff007

I know there are several methods to compare two closely related genomes; genotype. But almost all of them compare the stretch of matching sequences. For …
IGV related questions
written 5.6 years ago by wes •

1. May I know what is the triangle icon (between coverage and track file) in the IGV represent? ![enter image description here][1] 2. May I …
bcftools call always assigns a genotype even if there are no reads?
written 6.5 years ago by Candah

Hi, I am variantcalling my 96 multi sampled bam file with samtools/bcftools however I obtain some strange results. When I use the following command: bcftools …
how to extract per base information (in coverage track of IGV) from .bam file
written 7.6 years ago by xzhangxmu •

I would like to get coverage information per bases from the .bam file. But I don't know how to do it. I use IGV to …
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
written 8.9 years ago by Kevin Blighe

Thanks to brs1111 for the idea for this. If you have aligned your reads to a reference genome, here *hg38.fasta*, and want to know how …
vcf-annotate not adding annotations
written 9.5 years ago by wes3985 •

I would like to annotate a vcf file with the output of a filter that detects false positives. I know a very similar question to …
Need help understanding read depth for somaticsniper vcf's
written 12.1 years ago by Jordan

Hi, I'm having trouble understanding read depth in vcf's called by `somatic-sniper`. Here is a sample vcf file: ``` ##fileformat=VCFv4.1 ##fileDate=20140428 ##phasing=none ##reference=human_hg19.fa ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype …
Extract Allele At Particular Positions From Bam Files
written 12.4 years ago by guns.guru •

<p>Is there an easy way to extract the allele (monomorphic or polymorphic wrt the reference) for a sample across all reads at specific locations, given …
Interval Format Variant Files Convertion Problems And Igv And Annotation Application
written 12.8 years ago by Tonyzeng •

<p>I produced .sam formal variants files by Mpileup and then converted them into .bam. however, after several steps for filtering variants, I got interval format …