Entering edit mode
9.2 years ago
oritz1717
•
0
Hello,
I was wondering if it is possible with samtools to print solely the base pairs of an alignment. Right now, I have used samtools to print out a sam file in a specific region:
samtools view ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00099/alignment/HG00099.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam 17:7565097-7590856
The output of this is a massive file that prints out information like this (for many respective locations):
SRR062635.9218683 163 17 7565037 60 92M8S = 7565137 199
GGGATTACAGGCGGGAGCCACCGTGCCCGGCCTCCAGTATTTTGTTTATTTATTTTTTTTGAGACAGAGTCTCACTCTGTTGCACAGGCTGGGGGGCAGG
0LMMMMMNPPPPGQK@?9F9:C5<@DDD2F<D=CD+;868GFG>C??9GG@3GGGHCHBC78:B<KDIDDBFHGGGDFAAIK7GAEFED>F#########
X0:i:1 X1:i:0 XC:i:92 MD:Z:92 RG:Z:SRR062635 AM:i:37 NM:i:0 SM:i:37 MQ:i:60 XT:A:U BQ:Z:
@JH@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@@@@@@@@@
For my purposes, I was wondering if there is any way that I could just print out the base pairs (GGGATTTA etc.) without the other information.
Thanks,
Owen
That's both the appropriate UNIX command as well as a good response!
Thanks so much