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gatk-mouse-mm10.md

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Creating GATK mm10 resource bundle

The GATK resource bundle is a collection of standard files for working with human resequencing data. It contains known SNPs and indels to be used for BaseRecalibrator, RealignerTargetCreator, and IndelRealigner. This is an attempt to recreate a similar bundle for the mouse genome (UCSC build mm10).

For mouse SNPs, it's possible to use the dbSNP database, which should be comparable to the human version.

Download dbSNP GRCm38 VCF files (each chromosome is in a separate file):

wget --recursive --no-parent --no-directories \
--accept vcf*vcf.gz \
ftp://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/

Delete the non-primary chromosomes if they are not included in the reference FASTA file.

Add "chr" to each chromosome (convert from GRCm38 to mm10 format):

for vcf in $(ls -1 vcf_chr_*.vcf.gz) ; do
  vcf_new=${vcf/.vcf.gz/.vcf}
  echo $vcf
  zcat $vcf | sed 's/^\([0-9XY]\)/chr\1/' > $vcf_new
  rm -fv $vcf
done

Combine all dbSNP VCF files into one:

# generate parameter string containing all VCF files
vcf_file_string=""
for vcf in $(ls -1 vcf_chr_*.vcf) ; do
  vcf_file_string="$vcf_file_string -V $vcf"
done
echo $vcf_file_string

# concatenate VCF files
java -Xms16G -Xmx16G -cp ${gatk_path}/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants \
-R genome.fa $vcf_file_string -out dbsnp.vcf

More recent dbSNP releases include a merged 00-All.vcf.gz file in addition to the separate chromosome files. Although it will not need to be concatenated, it will likely still need to be adjusted for GATK compatibility.

For mouse indels, the Sanger Mouse Genetics Programme (Sanger MGP) is probably the best resource.

Download all MGP indels (5/2015 release):

wget ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz \
-O mgp.v5.indels.vcf.gz

Filter for passing variants with chr added:

# adjust header
zcat mgp.v5.indels.vcf.gz | head -1000 | grep "^#" | cut -f 1-8 \
| grep -v "#contig" | grep -v "#source" \
> mgp.v5.indels.pass.chr.vcf
# keep only passing and adjust chromosome name
zcat mgp.v5.indels.vcf.gz | grep -v "^#" | cut -f 1-8 \
| grep -w "PASS" | sed 's/^\([0-9MXY]\)/chr\1/' \
>> mgp.v5.indels.pass.chr.vcf

Sort VCF (automatically generated index has to be deleted due to a known bug):

java -Xms16G -Xmx16G -jar ${PICARD_ROOT}/picard.jar SortVcf VERBOSITY=WARNING \
SD=genome.dict \
I=mgp.v5.indels.pass.chr.vcf \
O=mgp.v5.indels.pass.chr.sort.vcf
rm -fv mgp.v5.indels.pass.chr.sort.vcf.idx

Additional info: