For those who didn't see it via email or twitter, samtools/htslib/bcftools version 1.3 have been released. There were a bunch of changes, though I'll just put a few of what I personally think are the major ones below:
- Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP and FTP, when HTSlib is configured to use libcurl for network file access rather than the included basic knetfile networking.
samtools faidxnow accept initial whitespace in ">" headers (e.g., "> chr1 description" is taken to refer to "chr1").
HTSlib's configure script and Makefile now fully support the standard convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed. Previously the Makefile listened to
$(LDLIBS)instead; if you were overriding that, you should now override LIBS rather than LDLIBS.
samtools sort in.bam out.prefixusage has been removed. If you are still using
out.prefix, convert to use
bamshufcommand has been renamed to
collate(hence the term bamshuf no longer appears in the documentation, though it still works on the command line for compatibility with existing scripts).
mpileupcommand now outputs the unseen allele in VCF/BCF as
<X>as previously, and now has AD, ADF, ADR, INFO/AD, INFO/ADF, INFO/ADR
--output-tagsannotations that largely supersede the existing DV, DP4, DPR annotations.
rmdupcommand no longer immediately aborts (previously it always aborted with bam_get_library() not yet implemented), but remains not recommended for most use.
index's optional index output path argument works again.
targetcut, and potential
mpileupsegfaults when given broken alignments with POS far beyond the end of their reference sequences.
statsnow outputs separate "N" and "other" columns in the ACGT content per cycle section.
samtools depthto show all locations, including zero depth sites.
samtools dictcommand, which creates a sequence dictionary (as used by Picard) from a FASTA reference file.
--target-regionsoption works again.
samtools fixmate - -works in pipelines again; with 1.0 to 1.2, this failed with [bam_mating] cannot determine output format.
samtools calmd -ubehaviour of writing compression level 0 BAM files. Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF BAM files, which cannot be read by most other tools. (Samtools commands other than
calmdwere unaffected by this bug.)
bcftools callhas new options
--ploidy-fileto make handling sample ploidy easier. See man page for details.
-eshort options changed to
-Eto be consistent with the filtering
--exclude) options used in other tools.
--threadsoption to control the number of output compression threads used when outputting compressed VCF or BCF.
polysomy: new commands for detecting CNVs, aneuploidy, and contamination from SNP genotyping data.
Congrats to the htslib, samtools, and bcftools developers on their fine work!