Hi samtools,
I'm trying to figure out why samtools mpileup gives different reference sequences for different bam files given that the bam were generated from alignment to the same reference genome (via STAR) and during mpileup I pass the same input bed and fasta.
I initially thought the issue stemmed from another program, but after troubleshooting see that it comes from samtools. Please see my comment on other github, which also contains example data; y9c/cpup#1 (comment)
And of course, if this is user error, please advise!
(run samtools --version)
$ samtools --version
samtools 1.18
Using htslib 1.18
Copyright (C) 2023 Genome Research Ltd.
Samtools compilation details:
Features: build=configure curses=yes
CC: gcc
CPPFLAGS: -I/apps/easybd/easybuild/software/cURL/8.0.1-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/XZ/5.4.2-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/zlib/1.2.13-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/ncurses/6.4-GCCcore-12.3.0/include
CFLAGS: -O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno -fPIC
LDFLAGS: -L/apps/easybd/easybuild/software/cURL/8.0.1-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/cURL/8.0.1-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/XZ/5.4.2-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/XZ/5.4.2-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/zlib/1.2.13-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/zlib/1.2.13-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/ncurses/6.4-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/ncurses/6.4-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/GCCcore/12.3.0/lib64 -L/apps/easybd/easybuild/software/GCCcore/12.3.0/lib
HTSDIR: htslib-1.18
LIBS: -lm -lpthread
CURSES_LIB: -lncursesw
HTSlib compilation details:
Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=no lzma=yes bzip2=yes plugins=no htscodecs=1.5.1
CC: gcc
CPPFLAGS: -I/apps/easybd/easybuild/software/cURL/8.0.1-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/XZ/5.4.2-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/zlib/1.2.13-GCCcore-12.3.0/include -I/apps/easybd/easybuild/software/ncurses/6.4-GCCcore-12.3.0/include
CFLAGS: -O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno -fPIC
LDFLAGS: -L/apps/easybd/easybuild/software/cURL/8.0.1-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/cURL/8.0.1-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/XZ/5.4.2-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/XZ/5.4.2-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/zlib/1.2.13-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/zlib/1.2.13-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/ncurses/6.4-GCCcore-12.3.0/lib64 -L/apps/easybd/easybuild/software/ncurses/6.4-GCCcore-12.3.0/lib -L/apps/easybd/easybuild/software/GCCcore/12.3.0/lib64 -L/apps/easybd/easybuild/software/GCCcore/12.3.0/lib -fvisibility=hidden
HTSlib URL scheme handlers present:
built-in: preload, data, file
S3 Multipart Upload: s3w, s3w+https, s3w+http
Amazon S3: s3+https, s3+http, s3
Google Cloud Storage: gs+http, gs+https, gs
libcurl: imaps, pop3, gophers, http, smb, gopher, ftps, imap, smtp, smtps, rtsp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict
crypt4gh-needed: crypt4gh
mem: mem
Please describe your environment.
- OS (run
uname -sr on Linux/Mac OS or wmic os get Caption, Version on Windows)
$ uname -sr
Linux 3.10.0-1160.81.1.el7.x86_64
- machine architecture (run
uname -m on Linux/Mac OS or wmic os get OSArchitecture on Windows)
- compiler (run
gcc --version or clang --version)
$ gcc --version
gcc (GCC) 12.3.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Hi samtools,
I'm trying to figure out why
samtools mpileupgives different reference sequences for different bam files given that the bam were generated from alignment to the same reference genome (via STAR) and during mpileup I pass the same input bed and fasta.I initially thought the issue stemmed from another program, but after troubleshooting see that it comes from samtools. Please see my comment on other github, which also contains example data; y9c/cpup#1 (comment)
And of course, if this is user error, please advise!
(run
samtools --version)Please describe your environment.
uname -sron Linux/Mac OS orwmic os get Caption, Versionon Windows)uname -mon Linux/Mac OS orwmic os get OSArchitectureon Windows)gcc --versionorclang --version)