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Re: [Samtools-help] indel file format question
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From: Adrian J. <ori...@gm...> - 2010-01-27 22:15:52
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Hi:
I was going to ask a similar question. What is:
H3764@B5?:F8(
F?4>@B;?4B76
G=C<>B>><F@>
in the example that Jessica described below.
Now my example:
chr1 13106026 T C 98 114 37 30 c$c$c$c$cCcccccccccccccCCCCCccccAC
GIIH0DF@>=HF7HHAFH8EHDB-GHHD2H
My understanding:
On chromosome 1 at position 13106026 , on reference there is T,
however on 29 of 30 tags have C and 1/30 has A.
c$c$c$c$cCcccccccccccccCCCCCccccAC - mean 4 tags has c end of read. Of
29 tags 7'C' are on forward strand. Whereas on others we see reverse
complement 'c' (that is G originally). - Am i correct?
Is samtools pileup format converts G to c for reverse strands (, strands)?
Also what is - GIIH0DF@>=HF7HHAFH8EHDB-GHHD2H
Could you please help me understand.
A screen shot of my example:
13106031 13106041 13106051
TGTTTCGAGGGCACTACAGCCAGAGCAATGGGAGG
C
c
c
c
c
c,
C.G
c,,,,
c,,,,,
c,,,,,,
c,,,,,,
c,,,,,,
c,,,,,,,,,,,,,
c,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,,,,
C..................
C..................
C...................
C...................
C...................
c,,,,,,,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,,,,,,,,
c,,,,,,,,,,,,,,,,,,,,,,,,,,
A......................................
C..................A...................
thank you.
Adrian
On Wed, Jan 27, 2010 at 11:44 AM, Heng Li <lh...@sa...> wrote:
> This question has been raised several times. I know add it to FAQ:
>
> http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_see_.60.2A.27_in_the_pileup_sequence_column._What_are_they.3F
>
> Heng
>
> On Wed, Jan 27, 2010 at 10:55:37AM -0500, Jessica Maia wrote:
>> Hi there,
>>
>> I have a question about the indel file format. Here's the indel file line:
>>
>> 1 52102 * -AC/-AC 37 159 27 13 -AC * 3 9 1
>>
>> In the 10th column in the indel file line is a (*) which is supposed to represent the second allele. Does the (*) refer to the reference allele?
>>
>> Here's the corresponding lines in the pileup file:
>> 1 52102 T T 66 0 27 13 .,$.,,..,.,-2ac,-2ac,+2ac,-2ac H3764@B5?:F8(
>> 1 52102 * -AC/-AC 37 159 27 13 -AC * 3 9 1
>> 1 52103 A A 54 0 26 12 ..,,..,.**,* F?4>@B;?4B76
>> 1 52104 C C 54 0 26 12 ..$,,..,.**,* G=C<>B>><F@>
>>
>> Thanks,
>>
>> Jessica
>>
>>
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