Question: i want to convert .ht2 files into FASTA file
0
gravatar for saumya.sharma1509
4 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 • 233 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by saumya.sharma15090

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

ADD REPLYlink written 4 months ago by genomax71k

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 4 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 4 months ago by genomax71k

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

ADD REPLYlink modified 4 months ago • written 4 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 4 months ago • written 4 months ago by genomax71k

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

ADD REPLYlink written 4 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 4 months ago by genomax71k

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 4 months ago by saumya.sharma15090

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

ADD REPLYlink written 4 months ago by WouterDeCoster41k

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

ADD REPLYlink written 4 months ago by saumya.sharma15090

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

ADD REPLYlink written 4 months ago by WouterDeCoster41k
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