Tag: wgs

After variants have been called, you may want to impute missing genotypes to get the most from your data. Harpy uses STITCH to impute genotypes, a haplotype-based method that is linked-read aware. Imputing genotypes requires a variant call file containing SNPs, such as that produced by and preferably filtered in some capacity. You can impute genotypes with Harpy using the module:

Raw sequences are not suitable for downstream analyses. They have sequencing adapters, index sequences, regions of poor quality, etc. The first step of any genetic sequence analyses is to remove these adapters and trim poor quality data. You can remove adapters, remove duplicates, and quality trim sequences using the module:

After reads have been aligned, e.g., with , you can use those alignment files (.bam) to call variants in your data. Harpy can call SNPs and small indels using bcftools mpileup or with freebayes. You can call SNPs with the module: