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Old 08-06-2014, 12:28 PM   #1
sscd
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Location: DC

Join Date: Aug 2014
Posts: 3
Default Pileup differences with different SAMtools versions

Hello,

Generating pileups of bacterial data sets with SAMtools 0.1.18 and 0.1.19, I have noticed differences in the pileup files. Version 0.1.18 produces pileups with greater depth. In both cases, the command line options are identical, just specifying the reference, the sample, and accepting defaults for all other options.

samtools mpileup -f reference.fasta reads.bam

Can anyone help explain what is causing the difference and offer best practice recommendations?

See examples of differences below.

Thanks!

samtools 0.1.18 pileup
seq1 4991 A 29 .C...,,,,,,,,,,,,+1t,..,+1t..tgg.gG !!1!!7@7A>8.0;1<.C@B+?9!#!-!!
seq1 4992 T 29 G..GG,,,,,,,,,,,,,..,..,,g.cG !90!!7@8@?;13=/4$C@A%>6&%!B!!
seq1 4993 G 29 A.$.AA,,,,,,,,,,,,,..,..,ac.a. !:1!!05,;@1/.60-,@CB(><-%!A!/
seq1 4994 G 28 ....,,,,,,,,,,,,,..,..,,a.,. !1!!3>/AE:4,5386A<<283,%!:!*
seq1 4995 A 29 GTGG,+1t,,+1t,,,,,,,,,,..,..,tg.t.^#c !&!!.:-=E24,5236ADB+<6,&!A!<!
seq1 4996 T 29 CACC,,,,,,,,,,,,,..,..,c,.c.a !%!!#9$4?-5*2/12>EC(58('3A#:!
seq1 4997 T 29 ..+5CACCG..,,,,,,,,,,,,,..,..,cc.g.g !%!!&@'>C28AB3=4E64,.,;',;$0!
seq1 4998 G 29 .$A.$.$,,,,,,,,,,,,,..,..,,,.,.c !!!!+9(1?.,97.3.><;&503)&@*5!
seq1 4999 G 27 C,,,,,,,,,,,,,..,..,,,.,.c^#, $,B77C:4@B290E424/-;1,7+/!!
seq1 5000 T 27 .,,,,,,,,,,,,,..,..,,,.,.,g +0B79C87A<190E6?42/;1,?+4!!

samtools 0.1.19 pileup
seq1 4991 A 18 .,,,,,,,,,,,,+1t,.... 17@7A>8.0;1<.C@B?9
seq1 4992 T 19 ..,,,,,,,,,,,,..... 907@8@?;13=/4C@A>6B
seq1 4993 G 18 .$.,,,,,,,,,,...... :105;@1/.60@CB><A/
seq1 4994 G 19 .,,,,,,,,,,,,..,... 13>/AE:45386A<<283:
seq1 4995 A 17 ,+1t,,,,,,,,,,...... .:=E245236ADB<6A<
seq1 4996 T 16 ,,,,,,,,,....,.. 94?52/12>EC583A:
seq1 4997 T 17 ,,,,,,,,,,,...,.. @>C28AB3=4E64.;;0
seq1 4998 G 17 ,,,,,,,,,,....,.. 91?.97.3.><;503@5
seq1 4999 G 20 ,,,,,,,,,,,,..,.,,.. B77C:4@B290E424/;17/
seq1 5000 T 22 ,,,,,,,,,,,,,..,..,,.. 0B79C87A<190E6?42/;1?4
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