v7.0.1

v7.0.1

This is a minor bug fix release. Two issues related to the evaluation of heterozygous rate within a sample have been corrected. First the CA genotype is now counted as a het, fixed by @sfacista and reported by @bryce-turner. Second the summarize.sh script was incorrectly excluding the first sample from the het rate calculation and plotting, fixed by @PedalheadPHX and discovered by @denriquez, we suspect this originated after an update to the java code removed the extra line from the snpSniffer.jar output.

What's Changed

• Changed awk parsing to include first data line to address issue 21
• Updated some aspects of readme by @sfacista in #18
• Updated Het.java, compiled snpSniffer.jar, and readme for issue 19 by @sfacista in #20

Full Changelog: v7.0.0...v7.0.1

Version v7.0.0

New Features

• Updated snpSniffer jar file
  • now outputs version with -version
  • now supports database.ini files with any size (no longer limited to exactly 387 query variants)
• New Summarize_snpSniffer.sh to replace old Run_snpSniffer script
  • This simplifies the code and outputs an additional graph to summarize the number of genotyped positions per sample

Version 2.0.0

Changes

• Updated genotyping script to leverage bcftools v1.0 or later. Removing the limitation that genotyping required old versions of samtools and bcftools from v0.19.0
• Refactored directory to create a folder for each genome

Genomes supported

• GRCh37/hg19 - Tested with hs37d5 used in TGen's b37 reference genome
• GRCh38/hg38 - Tested with hg38tgen which is identical to reference genome created by BWA.KIT or downloadable from Broad bundle

Limitations

• Custom SNP positions and database files can be created BUT the SNP test MUST be 387, it will not work otherwise
• For GRCh38/hg38 the contig names in the commonly used sequencing analysis pipelines have UCSC style contig names with a "chr" prefix. The -add step does not support the "chr" prefix. This is correct on the fly but the position and database files differ as the "chr" prefix is in the position file but not the database file.

Version 1 Release - b37, samtools <v1.0

This release supports GRCh37-hg19 and requires samtools v0.18 or v0.19, it DOES NOT work with samtools >= v1.0 due to changes is mpileup and bcftools functionality.