samtools 1.4 발표 - 설치 방법

안녕하세요

한주현입니다

12시간 전 samtools 1.4 버전이 나왔습니다 ㅎㅎㅎ

따끈따끈 하군요 ㅎㅎ

https://twitter.com/htslib/status/841334767798874113

과연 무엇이 좋아졌을까요??

https://github.com/samtools/samtools/releases/tag/1.4

jenniferliddle released this 14 hours ago

Release 1.4 (13 March 2017)

Noteworthy changes in samtools:
  
* Fixed Issue #345 - out-by-one error in insert-size in samtools stats

* bam_split now add a @PG header to the bam file
  
* Added mate cigar tag support to fixmate
  
* Multi-threading is now supported for decoding BAM and CRAM (as well
  as the previously supported encoding).  Most commands that read BAM
  or CRAM have gained an -@ or --threads arguments, providing a
  significant speed bonus.  For commands that both read and write
  files the threads are shared between decoding and encoding tasks.

* Added -a option to samtools mpileup to show all locations, including
  sites with zero depth; repeating the option as -aa or -a -a additionally
  shows reference sequences without any reads mapped to them (#496).

* The mpileup text output no longer contains empty columns at zero coverage
  positions.  Previously it would output "...0\t\t..." in some circumstances
  (zero coverage due to being below a minumum base quality); this has been
  fixed to output as "...0\t*\t*..." with placeholder '*' characters as in
  other zero coverage circumstances (see PR #537).

* To stop it from creating too many temporary files, samtools sort
  will now not run unless its per-thread memory limit (-m) is set to
  at least 1 megabyte (#547).

* The misc/plot-bamstats script now has a -l / --log-y option to change
  various graphs to display their Y axis log-scaled.  Currently this
  affects the Insert Size graph (PR #589; thanks to Anton Kratz).

* Fixmate will now also add and update MC (mate CIGAR) tags.

---

가장 눈에 띄는 것은 multithreading 이네요 ㅎㅎ

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

새로 나왔고 하니 이제 설치를 해보겠습니다 ㅎㅎ

참조 URL:

https://github.com/samtools/samtools/releases/tag/1.4

다운로드 URL:

https://github.com/samtools/samtools/releases/download/1.4/samtools-1.4.tar.bz2

이제 설치 하겠습니다

1) 압축해제

$ tar xf samtools-1.4.tar.bz2

2) 설치

$ make prefix=경로 install

설치과정

Makefile:102: config.mk: No such file or directory
config.mk:34: htslib-1.4/htslib_static.mk: No such file or directory
cd htslib-1.4 && make htslib.pc.tmp
make[1]: Entering directory `/home/jhan/Downloads/samtools-1.4/htslib-1.4'
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp

...

<생략>

...

install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /home/jhan/etc/samtools-1.4/bin
install -p -m 644 samtools.1 misc/wgsim.1 /home/jhan/etc/samtools-1.4/share/man/man1

확인

$ cd /home/jhan/etc/samtools-1.4/bin

$ ls -l

drwxr-xr-x 2 jhan jhan    4096  3월 14 14:05 ./
drwxrwxr-x 4 jhan jhan    4096  3월 14 14:05 ../
-rwxr-xr-x 1 jhan jhan   87351  3월 14 14:05 ace2sam*
-rwxr-xr-x 1 jhan jhan    5328  8월 19  2014 blast2sam.pl*
-rwxr-xr-x 1 jhan jhan    3364  8월 19  2014 bowtie2sam.pl*
-rwxr-xr-x 1 jhan jhan   18032  8월  1  2014 export2sam.pl*
-rwxr-xr-x 1 jhan jhan    6125  8월 19  2014 interpolate_sam.pl*
-rwxr-xr-x 1 jhan jhan   25464  3월 14 14:05 maq2sam-long*
-rwxr-xr-x 1 jhan jhan   25456  3월 14 14:05 maq2sam-short*
-rwxr-xr-x 1 jhan jhan   39827  3월 14 14:05 md5fa*
-rwxr-xr-x 1 jhan jhan   29259  3월 14 14:05 md5sum-lite*
-rwxr-xr-x 1 jhan jhan    6773  9월  2  2014 novo2sam.pl*
-rwxr-xr-x 1 jhan jhan   48659 10월  7 18:12 plot-bamstats*
-rwxr-xr-x 1 jhan jhan    3208  8월 19  2014 psl2sam.pl*
-rwxr-xr-x 1 jhan jhan    8961  8월 19  2014 sam2vcf.pl*
-rwxr-xr-x 1 jhan jhan 4413944  3월 14 14:05 samtools*
-rwxr-xr-x 1 jhan jhan   16478  8월 19  2014 samtools.pl*
-rwxr-xr-x 1 jhan jhan   11105  1월 28  2015 seq_cache_populate.pl*
-rwxr-xr-x 1 jhan jhan    3909  8월 19  2014 soap2sam.pl*
-rwxr-xr-x 1 jhan jhan    7888  8월 19  2014 varfilter.py*
-rwxr-xr-x 1 jhan jhan   61721  3월 14 14:05 wgsim*
-rwxr-xr-x 1 jhan jhan   12540 10월 15  2014 wgsim_eval.pl*
-rwxr-xr-x 1 jhan jhan    3583  8월 19  2014 zoom2sam.pl*

완료

$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.4 (using htslib 1.4)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     rmdup          remove PCR duplicates
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

multithreading 이 얼마나 빠를까 궁금하네요

그럼 다음에 봐요~