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.
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varsha619
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What make you think this reference doesn't work with Bowtie2? Do you encounter any errors? What were the steps you run?
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?
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.
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.
I have another question.
GATK Best Practices does not generate FASTQs. FASTQs are the input and come from the user.
Update: Yes, the Interleaved fastq file generated from unmapped BAMs (uBAMs) can be used as input for Bowtie2