Hi,
On Thu, Dec 10, 2015 at 10:01:47AM -0800, Richard Corbett wrote:
> Hi all,
> We have some old legacy scripts that rely on the old pileup format:
> ...
> 1 180934047 T 5 cccCc @JG>F
> 1 180934163 A 5 gGgGG GHJFF
> 1 180938117 G 4 .,.. JBJA
> ...
How does that differ to the current output from mpileup?
$ samtools mpileup -f hs37d5.fa 9827_2#49.bam
...
1 42744 C 2 ,, DE
1 42745 A 2 ,, DD
1 42746 C 3 ,,^!. CE;
1 42747 A 3 ,,. CIC
1 42748 A 3 ,,. BHB
1 42749 T 3 ,,+1a. CCD
1 42750 A 2 ,$. <E
1 42751 A 1 . E
1 42752 A 1 . D
This has the addition of ^ and $ markers for read start/finish, along
with various indel marks too, but I thought they were in the old
pileup format too. (If not then it's a trivial sed statment to remove
these.)
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
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