Question: Bowtie2 hg19 reference for gatk MuTect
0
gravatar for varsha619
14 months ago by
varsha61990
varsha61990 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 • 550 views
ADD COMMENTlink modified 14 months ago by h.mon31k • written 14 months ago by varsha61990

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 14 months ago by h.mon31k

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 14 months ago • written 14 months ago by varsha61990

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 14 months ago • written 14 months ago by igor11k

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 14 months ago • written 14 months ago by varsha61990
2
gravatar for igor
14 months ago by
igor11k
United States
igor11k wrote:

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

ADD COMMENTlink written 14 months ago by igor11k

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

ADD REPLYlink written 14 months ago by varsha61990
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 14 months ago by genomax89k
1
gravatar for h.mon
14 months ago by
h.mon31k
Brazil
h.mon31k 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 14 months ago • written 14 months ago by h.mon31k

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

ADD REPLYlink written 14 months ago by varsha61990
0
gravatar for swbarnes2
14 months ago by
swbarnes28.6k
United States
swbarnes28.6k 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 14 months ago by swbarnes28.6k

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

ADD REPLYlink written 14 months ago by varsha61990
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