Convert output maq to vcf
Hi,
I try to use output maq to analize with snpEff, but i need convert the output maq to vcf.
There is some converter, because maq is something old.
Thanks.
snp
• 1,257 views
•
link
written
by
jfnarvaezp •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Convert SHAPEIT haps file to vcf
written by michael.flower.14 •I've phased some sequencing using SHAPEIT, producing two files: 125QiPSC.haps 125QiPSC.log I would now like to subset the file for my SNPs of interest. To …
-
Convert VCF4.1 to VCF4.2 using bcftools (preferrably)
written by nikitavlassenkoI need to convert **VCF4.1** to **VCF4.2**, and I am using **bcftools**. There is the method called convert but I am not sure how to …
-
Annotating varscan2 output
written by ar.satkhol18 •Hi, I have a vcf file of somatic variants from Varscan2. I tried annotating it with Variant Effect Predictor and snpEff. The online version of …
-
VCF file (annotated with snpeff) to MAF
written by JJHi all, I've read the posts here on VCF to MAF conversion (e.g. https://www.biostars.org/p/74822/ ). However, I could not manage to convert a snpeff annotated …
-
SNP annotation using gff3
written by rezahi everyone i am trying to annotate of identified SNPs and INDELs (vcf format) using software such as snpEff. i downloaded gff3 file correspond to …
-
Availability of a robust, annotation-aware vcf-to-json converter
written by Sean DavisIs anyone actively using a vcf-to-json converter that you would recommend? I am aware of Variant Effect Predictor's ability to output json, but I am …
-
SnpEFF generates value as true instead of 1
written by winI am using SNPEff to annotate our VCF files and it is working fine. But the issues is that at certain annotations it generates a …
-
Converting VarScan output (.txt) format to .vcf for annotation
written by ivivek_ngs<p>Dear All,</p> <p>Is there any script available that will help me to convert the VarScan output in .txt format to .vcf format which I can …
-
Maq Output To Bed File
written by Sara •<p>Hi,</p> <p>I want to convert map-view file (output of Maq) to bed file.</p> <p>is there any option in Maq I should consider?</p> <p>Thanks in advance …
-
Mounting A File System On Amazon Web Services
written by Peter •<p>Hi,</p> <p>I'm trying to use an Amazon Web Server linux instance to do some bioinformatics work. I believe I have setup an attached storage area …