sam2tsv用法

sam2tsv主要可以将sam文件转为tab分割的tsv文件

sam2tsv安装

git clone "https://github.com/lindenb/jvarkit.git"
cd jvarkit
./gradlew sam2tsv

或者使用conda安装

conda install -c hcc jvarkit-sam2tsv

Usage: sam2tsv [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
-r, -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
-N, --skip-N
Skip 'N' operator
Default: false
--version
print version and exit

使用方法：

java -jar dist/sam2tsv.jar -R genome.fa test.bam 

#Read-Name  Flag  MAPQ  CHROM  READ-POS0  READ-BASE  READ-QUAL  REF-POS1  REF-BASE  CIGAR-OP
r001        163   30    ref    0          T          .          7         T         M
r001        163   30    ref    1          T          .          8         T         M
r001        163   30    ref    2          A          .          9         A         M
r001        163   30    ref    3          G          .          10        G         M
r001        163   30    ref    4          A          .          11        A         M
r001        163   30    ref    5          T          .          12        T         M
r001        163   30    ref    6          A          .          13        A         M
r001        163   30    ref    7          A          .          14        A         M
r001        163   30    ref    8          A          .          .         .         I
r001        163   30    ref    9          G          .          .         .         I

#sam2tsv can read data from a linux pipe.
samtools view -h input.bam | java -jar dist/sam2tsv.jar

参考：https://lindenb.github.io/jvarkit/Sam2Tsv.html