Just read the help screen,
samtools view -o OUTFILE BAM_FILE.bam
should do what you want.
best,
Sven
2016-03-18 4:47 GMT+01:00 Robert May <[email protected]>:
> Linux Mint desktop Mate USB Drive
> samtools viewI get it to print
> samtools view [options] <in.bam>|<in.sam> [region1 [...]]
>
> how do I get it to print to a file?
>
> samtools view -h -o in.bam
> reprints options list and command usage
>
> remove -o or -h -o
> prints to screen which takes forever
>
> samtools view -h -o in.bam [ChrY:1-30000000]
> open: No such file or directory
> [main_samview] fail to open "[ChrY:1-30000000]" for reading.
>
> remove -h and -o remove -h same results
>
> remove -o
> starts to print to screen then
> @PG ID:aengine-align PN:aengine
> CL:/opt/ngs_tools/sw/aengine/bin/aengine align
> /opt/ngs_tools/ref/hg19/ucsc.hg19.fasta -f
> /tmp/53336e186c696e47beba0000.aligned20140327-22892-1j01jqr.bam
> /mnt/star01/hiseq/archive/2500/45978_2500A_9pM_H93KGADXX/HiYNGS-5705701/GRC12122101-45978-B4-8566586/GRC12122101_S16_L001_R1_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/45978_2500A_9pM_H93KGADXX/HiYNGS-5705701/GRC12122101-45978-B4-8566586/GRC12122101_S16_L001_R2_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/45978_2500A_9pM_H93KGADXX/HiYNGS-5705701/GRC12122101-45978-B4-8566586/GRC12122101_S16_L002_R1_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/45978_2500A_9pM_H93KGADXX/HiYNGS-5705701/GRC12122101-45978-B4-8566586/GRC12122101_S16_L002_R2_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/49416_2500B_9-5pM_H8U44ADXX/HiYNGS-5705701/GRC12122101-49416-B12-7979039/GRC12122101_S33_L001_R1_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/49416_2500B_9-5pM_H8U44ADXX/HiYNGS-5705701/GRC12122101-49416-B12-7979039/GRC12122101_S33_L001_R2_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/49416_2500B_9-5pM_H8U44ADXX/HiYNGS-5705701/GRC12122101-49416-B12-7979039/GRC12122101_S33_L002_R1_001.fastq.gz
> /mnt/star01/hiseq/archive/2500/49416_2500B_9-5pM_H8U44ADXX/HiYNGS-5705701/GRC12122101-49416-B12-7979039/GRC12122101_S33_L002_R2_001.fastq.gz
> --match-score 1 --mismatch-penalty 4 --gap-open-penalty 6
> --gap-extension-penalty 1 --gap-open-penalty-min 4
> --gap-extension-penalty-min 0.75 --min-repeat-len 3 --max-repeat-len 6
> --log /mnt/star01/hiseq/scratch/inset/bigy/GRC12122101/align.log
> VN:v0.3-50-gd89e451
> @PG ID:aengine-postprocess PN:aengine
> CL:/opt/ngs_tools/sw/aengine/bin/aengine postprocess
> /opt/ngs_tools/ref/hg19/ucsc.hg19.fasta
> /tmp/53336e186c696e47beba0000.aligned20140327-22892-1j01jqr.bam -f
> /tmp/53336e186c696e47beba0000.pp20140327-22892-tmut9w.bam --match-score 1
> --mismatch-penalty 4 --gap-open-penalty 6 --gap-extension-penalty 1
> --gap-open-penalty-min 4 --gap-extension-penalty-min 0.75 --min-repeat-len
> 3 --max-repeat-len 6 --log
> /mnt/star01/hiseq/scratch/inset/bigy/GRC12122101/postprocess.log
> --tmp-file-path /tmp VN:v0.3-50-gd89e451
> @PG ID:aengine-sort PN:aengine
> CL:/opt/ngs_tools/sw/aengine/bin/aengine sort -f
> /mnt/star01/hiseq/scratch/inset/bigy/GRC12122101/GRC12122101.bam
> /tmp/53336e186c696e47beba0000.pp20140327-22892-tmut9w.bam --log
> /mnt/star01/hiseq/scratch/inset/bigy/GRC12122101/markdupes.log
> --tmp-file-path /tmp --mark-duplicates VN:v0.3-50-gd89e451
> [bam_parse_region] fail to determine the sequence name.
> [main_samview] region "[ChrY:1-30000000]" specifies an unknown reference
> name. Continue anyway.
>
>
>
>
> .
>
>
>
>
>
> Bob May
> DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler
> Surname and ISOGG YTree
>
>
> ------------------------------------------------------------------------------
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