Calling SNPs¶

If you have a sample and you want to have one-stop-shop analysis run the following:

$ phenix.py run_snp_pipeline \
-r1 <path to R1.fastq> \
-r2 <path to R2.fastq> \
-r <path to reference> \
--sample-name <NAME> \
--mapper bwa \
--variant gatk \
--filters min_depth:5,mq_score:30 \
-o <path to output directory>

This will map with BWA and call variants with GATK. Intermediate files are written into the specified output directory. –sample-name option is very important, it specifies what output files will be called and the read group in the BAM file. If you omit it, test_sample will be used.

Config¶

If you have a pipeline, or want to run the same settings for different samples this process can be simplefied by having a single config file. The file is in YAML format and takes common options that may be used for all samples:

mapper - string
mapper-options - string
variant - string
variant-options - string
filters - dictionary
annotators - list

Below is an example of config file:

mapper: bwa
mapper-options: -t 4
variant: gatk
variant-options: --sample_ploidy 2 --genotype_likelihoods_model SNP -rf BadCigar -out_mode EMIT_ALL_SITES -nt 1
filters:
  ad_ratio: 0.9
  min_depth: 5
  qual_score: 30
  mq_score: 30
annotators:
  - coverage