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sort variant_calling into mapping using bwa and variant calling

Status: Open.

#40 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Mar 23, 2023

compare haplotype output from reads mapped using bbsplit vs. bwa

Status: Open.

#39 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Mar 22, 2023

Get summary file of reads before running censoring

Status: Open.

#35 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Mar 17, 2023

Have snakemake submit jobs for each rule

Status: Open.

#34 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Mar 17, 2023

Add more details to documentation about reference and primers

Status: Open.

#23 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Aug 23, 2022

Refactor step1 into multiple steps

Status: Open.

#19 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Aug 23, 2022

Clarify what columns in <code>trackReadsThroughPipeline</code> contain

Status: Open.

#15 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Apr 21, 2022

Only store fastq files in one place

Status: Open.

#9 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Apr 21, 2022

Document how to use pipeline

Status: Open.

#1 In kathiehuang/haplotype_calling_pipeline;

· zenalapp opened on Mar 31, 2022