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 
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