samtools 1.17
Using htslib 1.17
Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=no lzma=yes bzip2=yes plugins=no htscodecs=1.4.0
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -g -O2 -fvisibility=hidden
LDFLAGS: -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
samtools consensus -a -f fasta --region chr1 --show-del no --show-ins no -m simple bamfile-input.bam -o consensus-output-mm10.fa
Great tool and Works fine with the 'simple' consensus algorithm (chr1 test: 195471971 bases) and serves the purpose well.
Issue:
samtools consensus -a -f fasta --region chr1 --show-del no --show-ins no -m bayesian bamfile-input.bam -o consensus-output-mm10.fa
Running with 'bayesian' or 'bayesian_116' resulted in 195471200 bases and also slightly lower number of bases for all chromosomes (without --region). Missing bases look like distributed along the chromosome. Reads were aligned to mm10 using Bowtie2. Not sure, if this difference is due to compilation or environment (same error with SAMtools/1.16.1-GCC-11.3.0).
'bayesian' algorithm being the default might be misleading for generating consensus sequences that are perfectly aligned with the reference genome. And, it would be great to have the 'bayesian' option. Thanks.
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