v1.4.2 Release

1. Add split_interval_list_to_bed_helper.pl
2. Use "-w 30 -T 4" in pindel_helper.pl
3. Set filter column with "." if set_filter_flag is false.

minor updates to docm, filters

Merge pull request #89 from chrisamiller/master

handles gzip files, simplifies some variable naming

long overdue

long overdue release with like two pages of commits. They include:

• new deps for cyvcf and a mapq0 filter
• update vcf_annotation_tools
• fgbio and UMI support
• upgraded picard and gatk
• bugfixes

Version 1.3.0 release

1. Only report variant positions in varscan germline.
2. Add single_sample_docm_filter.pl
3. Replace empty string with 0 for AD, DP, AF and round AF values to 3 decimal places in add_bam_readcount_to_vcf_helper.py

Version 1.2.0 release

1. add add_bam_readcount_to_vcf_helper.py
2. upgrade Picard 2.4.1 -> 2.14.0

Version 1.1.0 release

1. Add docm_and_coding_indel_selection.pl
2. Modify bam_readcount_helper.py to make empty files if no snvs/indels bam_readcount lines.

Bug Fix: Handle VEP annotated SVs

See #49 for details.