Question: How to annotate position with reference
0
gravatar for tongshiyuan
16 months ago by
tongshiyuan0 wrote:

Hi,
If I have a file like:

CHR POS
1 10001
1 10002
1 10003
1 10004
1 10005
1 10006
...

How can I annotate it with reference? just like:

1 10001 A
1 10002 T
1 10003 C
1 10004 G
1 10005 A
1 10006 G
...

dna position annotate • 257 views
ADD COMMENTlink modified 16 months ago by Pierre Lindenbaum130k • written 16 months ago by tongshiyuan0

Did you try some of these solutions?

ADD REPLYlink written 16 months ago by Benn8.0k
2
gravatar for Pierre Lindenbaum
16 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

$ cat jeter.tsv RF01 101

RF01 102
RF01 103
RF01 104
RF01 105
RF01 106 



$ cat jeter.tsv | while read  A B; do echo -n "$A $B " && samtools faidx rotavirus_rf.fa "${A}:${B}-${B}" | grep -v '^>' ; done
RF01 101 A
RF01 102 T
RF01 103 T
RF01 104 C
RF01 105 T
RF01 106 T
ADD COMMENTlink written 16 months ago by Pierre Lindenbaum130k
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