Question: Bowtie2 hg19 reference for gatk MuTect
0
gravatar for varsha619
12 days ago by
varsha61980
varsha61980 wrote:

Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and using hg19 Bowtie2 index from http://bowtie-bio.sourceforge.net/bowtie2/index.shtml gives a compatibility error with dbsnp_138.hg19.vcf file while running GATK MuTect.

ERROR MESSAGE: Input files dbsnp_138.hg19.vcf and reference have incompatible contigs: No overlapping contigs found.

Is there any way to fix this other than switching to the bwa aligner? Is there a different reference or dbsnp vcf file I could use? Thank you for your help.

bowtie2 gatk • 154 views
ADD COMMENTlink modified 12 days ago by h.mon26k • written 12 days ago by varsha61980

The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2

What make you think this reference doesn't work with Bowtie2? Do you encounter any errors? What were the steps you run?

ADD REPLYlink written 12 days ago by h.mon26k

This is the error I get with the fasta file I downlaoded from - ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/

bowtie2 -p 4 -x ucsc.hg19.fasta -1 R1_001.fastq.gz -2 R2_001.fastq.gz | samtools view -bS - > 001_out.bam

(ERR): "ucsc.hg19.fasta" does not exist or is not a Bowtie 2 index

Exiting now ...

[samopen] no @SQ lines in the header.

[sam_read1] missing header? Abort!

Do I need to create new indices to be able to use this reference file from the GATK bundle with bowtie2?

ADD REPLYlink modified 12 days ago • written 12 days ago by varsha61980

If you download the sequence from one source and the index from a different source, it is not surprising that they are not be compatible.

ADD REPLYlink modified 12 days ago • written 12 days ago by igor8.0k

I did keep the reference files consistent through the steps. I meant to say that I tried using both files separately. I can successfully align the files using hg19 Bowtie2 indices but then I get a compatibility error in MuTect with dbsnp_138.hg19.vcf file while running GATK MuTect. If I try to use the reference in GATK bundle to align instead, I get the error: file does not exist or is not a Bowtie 2 index.

ADD REPLYlink modified 12 days ago • written 12 days ago by varsha61980
2
gravatar for igor
11 days ago by
igor8.0k
United States
igor8.0k wrote:

Since GATK does not provide a Bowtie2 index, the index does not exist. Thus, you need to generate it yourself.

ADD COMMENTlink written 11 days ago by igor8.0k

Yes this fixed the issue, my bad. Thank you!

ADD REPLYlink written 10 days ago by varsha61980
1

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

ADD REPLYlink written 10 days ago by genomax69k
1
gravatar for h.mon
12 days ago by
h.mon26k
Brazil
h.mon26k wrote:

Do I need to create new indices to be able to use this reference file from the GATK bundle with bowtie2?

Yes, creating the bowtie2 indices would help.

ADD COMMENTlink modified 12 days ago • written 12 days ago by h.mon26k

Worked after I created the bowtie2 indices for the GATK bundle hg19 genome file, thank you.

ADD REPLYlink written 10 days ago by varsha61980
0
gravatar for swbarnes2
12 days ago by
swbarnes26.0k
United States
swbarnes26.0k wrote:

Input files dbsnp_138.hg19.vcf and reference have incompatible contigs

Okay, so did you do the obvious thing and check to see that chromosome names are the same between the two files?

ADD COMMENTlink written 12 days ago by swbarnes26.0k

Yes both the files have the format chr1, chr2, ...

ADD REPLYlink written 12 days ago by varsha61980
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