Skip to content

Latest commit

 

History

History
35 lines (25 loc) · 3.31 KB

README.variant_calling.md

File metadata and controls

35 lines (25 loc) · 3.31 KB
Raw

Variant Calling Pipeline

If you'd like to run the variant calling pipeline on its own, you should provide required input in configs/config-variant_calling.yaml.

Inputs

  • FASTQ files containing DNA sequencing reads for each sample. Specify the location of these files in a tab delimited text file containing three columns: unique_sample_name | dna_fastq_path_1 | dna_fastq_path_2 where each row is a different sample.
  • A reference genome for DNA-seq alignment
  • A BWA index of the aforementioned reference genome

Other Inputs and Options

  • If you choose to use GATK's base quality (BQSR) and variant quality (VQSR) score recalibration, you must provide the following, as described in this GATK article:

    • True sites training resource: HapMap
    • True sites training resource: Omni
    • Non-true sites training resource: 1000G
    • Known sites resource, not used in training: dbSNP

    These resources can usually be easily obtained from the GATK resource bundle.

    You will also be required to specify a target sensitivity value, as described in a previously mentioned GATK article.

  • If you choose not to perform VQSR, the pipeline will default to hard filtering your variants. You will need to provide a GATK filter expression, as described in this GATK article. One example might be "QD < 2.0 || FS > 60.0 || MQ < 40.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0".

Running the variant calling pipeline on its own

When calling Snakemake, use options -s and --configfile to specify the location of the Snakefile and its corresponding config file. We also recommend using the --use-conda option to let Snakemake handle all dependencies of the pipeline.

snakemake -s Snakefiles/Snakefile-variant_calling --configfile configs/config-variant_calling.yaml --use-conda

Output

The variant calling pipeline creates the following directories under the output directory specified in your config file. The genotypes folder will contain the final output, a filtered VCF containing heterozygous SNPs for all samples.

  • dna_align - output from BWA and samtools
  • base_recal - output from GATK's BQSR
  • haplotype - output from GATK's Haplotype Caller and a file ALL.genotype.vcf.gz containing genotyped variants for all samples
  • variant_filter - output from variant filtering (either VQSR or hard filtering) of SNPs
  • genotypes - heterozgyotes from the filtered VCF