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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