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finding compatible version of reference genome for use of GATK

I am mapping a series of fastq files, containing ChiP-Seq data, with bowtie2 (my mapping software of choice) to the GRCh37 genome: https://www.gencodegenes.org/human/release_39lift37.html . I have mapped as follows:

bwa mem GRCh37.primary_assembly.genome.fa ${srr}.fastq.gz | samtools view -S -b -q 10 - > ${srr}.bam

I then create the fasta file for the bt2 reference and index it:

samtools faidx GRCh37.primary_assembly.genome.fa
java -jar ~/picard.jar CreateSequenceDictionary -R GRCh37.primary_assembly.genome.fa

However, when I then try to call variants in this data I get an error:

java -jar ~/picard.jar MarkDuplicates -I ${srr}_sorted.bam -M metrics.txt -O ${srr}_sorted_dedup.bam
gatk --java-options "-Xms10G -Xmx10G -XX:ParallelGCThreads=2" BaseRecalibrator \
    -I ${srr}_sorted_dedup.bam \
    -R GRCh37.primary_assembly.genome.fa \
    -O ${srr}_sorted_dedup.report \
    --known-sites variants.vcf

The marking of the duplicates part seems to work fine but for the recalibrating the bases part the contigs do not seem to match up:

A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found 

contigs with the same name but different lengths:
  contig reference = 10 / 135534747
  contig features = 10 / 135284542.
   reference contigs = [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1, 20, 21, 22, 2, 3, 4, 5, 6, 7, 8, 9, MT, X, Y]
   features contigs = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, XY, M]

I have read that the vcf file that I am using was made according to GRCh37: https://www.synapse.org/#!Synapse:syn10901595

I downloaded the plink files from https://www.synapse.org/#!Synapse:syn17008939 and made the vcf file as follows:

plink --bfile ROSMAP_data --recode vcf --output-chr M

Hence I am wondering how the vcf file can mismatch the ref genome when they are the same- has anyone experienced this problem before?

Also just check that the ref genome should not be b37 does anyone know of a link to the b37 fasta file? The following link which I tried- leads to a NO PERMISSION page for me:

https://console.cloud.google.com/storage/browser/_details/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta;tab=live_object
bowtie2 gatk
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updated by Divon • Divon • written by chrisclarkson100 chrisclarkson100

4 answers

I solved this problem by finding the correct liftover chain file to convert my vcf/known-sites file to a version that was compatible with my reference genome. The README that described the making of this vcf file states that it was created using the GRCh37 genome as the reference- when in fact it was the b37 genome- hence:

java -jar picard.jar LiftoverVcf \\
 I=variants.vcf \\
 O=lifted_over.vcf \\
 CHAIN=b37tohg19.chain \\
 REJECT=rejected_variants.vcf \\
 R=GRCh37.primary_assembly.genome.fa

And then the base recalibration step worked.

NOTE: The chain file is downloaded from https://github.com/broadgsa/gatk/tree/master/public/chainFiles

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written by chrisclarkson100 chrisclarkson100

the reference/bam file have a different sequence dictionary than the VCF file ( for example there is chromosome "M" vs "MT" ). Both files should use the very same dictionary/reference.

https://www.google.com/search?q=%22Input+files+reference+and+features+have+incompatible+contigs%22

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written by Pierre Lindenbaum Pierre Lindenbaum

To avoid issues due to incompatibility between files when using GATK tools, download the resource files (e.g. genome FASTA/ dict) from https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle.

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written by cherweiyuan • cherweiyuan

You could use Genozip (of which I am the author) to update the VCF file's CHROMs to match those of the reference file:

genozip --match-chrom-to-reference --reference <ref-file> myfile.vcf
genocat myfile.vcf.genozip

See: https://genozip.com/genozip.html and https://genozip.com/vcf.html

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written by Divon • Divon

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