Question: i want to convert .ht2 files into FASTA file
0
gravatar for saumya.sharma1509
14 months ago by
saumya.sharma15090 wrote:

Hey,

I want to convert .ht2 files into FASTA file. as I have obtained .ht2 files from Hisat2 tool and now I need to convert these files into fasta format please help? these .hts2 files are obtained as I have indexed my reference genome. now, I am calling haplotypecaller from GATK tools for haplotypes and it needs INDEXED reference genome as I have .hts2 index files.GATK is not accepting those files as it only accepts fasta file. please guide me?

P.S- after running hisat2, there are 8 resulting files.

hisat2 tool gatk fasta • 561 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by saumya.sharma15090

If you still have your original reference why do you need to do this conversion?

ADD REPLYlink written 14 months ago by genomax87k

because GATK haplotypecaller needs fasta file of the indexed reference genome. if I am indexing my reference file again from samtools it says "not supported file format". so I think I need to convert the indexed files which I have obtained from hisat2 into FASTA file.

if you could suggest any other way to call haplotypes from vcf files. Please suggest?

ADD REPLYlink written 14 months ago by saumya.sharma15090

if I am indexing my reference file again from samtools it says "not supported file format".

samtools index ref.fa is generating that error?

ADD REPLYlink written 14 months ago by genomax87k

it generates a ".fai" file but when I use that file on GATK it says not supported file format.

ADD REPLYlink modified 14 months ago • written 14 months ago by saumya.sharma15090

You need to create .dict file.
Also see @Pierre's answer: Why do we need a .fai file and a .dict file of the reference during alignment and variant calling using GATK?

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax87k

I have created a ".dict" file from picard tools. but then I have the error

ADD REPLYlink written 14 months ago by saumya.sharma15090

Just to be sure you used the same version of GATK to make the .dict file as one you plan to use?

ADD REPLYlink written 14 months ago by genomax87k

okayyy...can you please guide me any other way to find haplotypes? is there any way to obtain haplotypes from a vcf file? please provide me with the command for making ".dict file"?

can you make me clear about the gatk command? I have to input ".dict file" "fai.file" while using the command or I have to just put these files into the same directory while running the command? P.S- I am working on ubuntu

ADD REPLYlink written 14 months ago by saumya.sharma15090

Those files should just be in the same directory as your fasta file

ADD REPLYlink written 14 months ago by WouterDeCoster44k

in command which file will be used? the original reference genome or .dict file or .fai file?

ADD REPLYlink written 14 months ago by saumya.sharma15090

GATK uses the fasta file as input, and expects the other files to be present.

ADD REPLYlink written 14 months ago by WouterDeCoster44k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1796 users visited in the last hour