weird samtools pileup bug

[xiang]

19 33769843 * */+TCTC 29 29 42 3 * +TCTC 2 1 0 0 0
19 33776199 * */-TTT 90 90 49 8 * -TTT 6 2 0 0 0
19 33778072 T TT 63 0 42 12 ,,,..,,.,,.. >?<8>=?=,5@@
19 33841537 * */-AAA 2 2 49 12 * -AAA 11 1 0 0 0
19 33845663 * */-TTTTTTTTTTTTT 151 151 46 13 * -TTTTTTTTTTTTT 10 3 0 0 0

It then pass samtools varfilter, and was reported as SNP and crashed my pipeline. Anyone has idea about this?

[lh3]

Interesting. It is the first time someone reports such a problem, and I do not see any chance that this may happen. Can you get the alignment between 19:33778000-33778150 and post it here? Thanks.

[xiang]

The bad thing is I deleted the sam files after I got the result of "samtools varFilter" due to the space limitation in farm. I have done a local pileup, it seems that the result is different, even the number of reads covering that region.

I am rerunning my pipeline to see whether I can catch it agin..


19 33778065 A A 22 0 0 26 .,,.,,,.,,,.,,,,.,,,,,.,., ABBC>?BB??;A;<<B>A@97AA8B2
19 33778066 T T 3 0 0 26 .,,.,,$,.,,,.,,,,.,,,,,.,.g C9.B2?@B?=1@2?<B>=@92AA)B'
19 33778067 T T 23 0 0 25 .,,.,,.,,,.,,,,.,,,,,.,., C@>B8BB>?,A7<<@>@@97=B9B2
19 33778068 G G 23 0 0 25 .,,.,,.,,,.,,,,.,,,,,.,., BAAB>AC?=;A;?<B<:A>:BA%B8
19 33778069 C C 23 0 0 25 .,,.,,.,,,.,,,,.,,,,,.,., B@@A>AB?;3A+@>@<@@>8BA)B.
19 33778070 T T 23 0 0 25 .,,.,,.,$,,.,,,,.,,,,,.,., BB2B>@C>2>A+;>B>=@>>AA6B2
19 33778071 C C 23 0 0 24 .,,.,,.,,.,,,,.,,,,,.,., AB<A<@C=@A)@>B7@B>>>A6B;
19 33778072 T T 23 0 0 24 .,,.,,.,,.,,,,.,,,,,.,., BB>A5AC=@A7?>B<@B>>AA6B=
19 33778073 G G 23 0 0 25 .,,.,,.,,.,,,,.,,,,,.,.,^!, BB8A<AC?9B<?>B><@>>AA3B>?
19 33778074 T T 23 0 0 26 .,,.,,.,,.,,,,.,,,,,.,.,,^!. BB=?5A;;?@:A>B<@B><A@8B;AB
19 33778075 A A 22 0 0 27 .,,.,,.,,.,,,,.,,,,,.,.,,.^!, @2<?1A==6A<?>B9AB>>AA3B;AB8
19 33778076 G G 22 0 0 27 .,,.,,.,,.,,,,.,,,,,.,.,,., A4A8<?@?=B6@>B<@@>>AA7B8@B<
19 33778077 T T 22 0 0 27 .,,.,,.,,.,,,,.,,,,,.,.,,., >@?>,AB=@?4@>B-AA>>@@6@;>B:
19 33778078 A A 22 0 0 28 .,,.,,.,,.,,,,.,,,,,.,.,,.,^!, B=BB7AC?@A&?>B:AB>>@B3B9AB<6
19 33778079 A A 22 0 0 28 .,,.,,.,,.,,,,.,,,,,.,.,,.,, B@AB>@@=?@;@>B7@B>>?A9B<9B<0

[xiang]

I have finished the re-running. Surprisingly, the bug disappeared. I diff two files. Here is the difference. Apparently, several entries appeared around the buggy region. So I think the problem is caused by the hard-disk failure which I knew it happened indeed. Sorry for claiming it is a bug of samtools.


< 19 33785231 R A 61 61 48 17 a$aaAaaaAAGaaAaaAA BCC@BCB=B0A<B><CB
< 19 33785365 Y T 15 15 43 9 TTtTcccTc =+C@<BAC*
< 19 33788856 * */-ACAA 11 11 23 9 * -ACAA 8 1 0 0 0
< 19 33789802 * -C/* 14 33 11 6 -C * 1 5 0 0 0
< 19 33790371 * */+A 49 49 29 11 * +A 9 2 0 0 0
< 19 33792837 * */+TG 14 14 33 8 * +TG 7 1 0 0 0
< 19 33797007 * */-TGGTATATGCACTTAC 297 297 20 15 * -TGGTATATGCACTTAC 10 5 0 0 0
< 19 33798324 * -A/-A 10 37 39 4 -A * 2 2 0 0 0
< 19 33799825 G A 33 81 28 24 A$AAA,,aAAaa,AaA..aaAa^;A^!.^<A +@=@@???AA>9>@A>>>>C;+C+
< 19 33802844 M C 27 27 25 18 aAaccCcTcCCCcCCCCc B8B/5CC+@CBB;BCB=>
< 19 33803355 G A 47 90 26 26 AAaaaA,aAa.aaaaaA,a,aAAaa, =?6C<=,>>:><C?=>=0;==>>2<;
< 19 33810370 R G 34 34 28 13 AgggggAgGggGg 8BACBA7=7>2B<
< 19 33810474 C Y 11 11 32 14 ,T......,T,t.T B>6=6@<9FA:5><
< 19 33810840 M A 52 52 29 13 AaaaAAAcaagaA ?>CC6B@%?='7A
< 19 33810942 * */-AAA 23 23 41 5 * -AAA 4 1 0 0 0
< 19 33810962 C M 5 5 42 10 A.AA,..,.. @2<+7>BA:B
< 19 33812469 * */-A 117 117 40 13 * -A 12 1 0 0 0
< 19 33814444 * */-TCACCAGAAAATTTTG 75 75 14 13 * -TCACCAGAAAATTTTG 11 2 0 0 0
< 19 33821778 G A 84 84 28 19 AAAAAAAAaAAAAaaaaa^?A .B31?ABB?CABB77;<7C
< 19 33821992 * */-AGTT 11 11 21 9 * -AGTT 8 1 0 0 0
< 19 33822530 R A 2 2 31 33 aaaAaAAaaAAgaaAAGagAAagggAgAAAgag ?>?/A=B>>.A<?>9?<>?A?=(47?7>0?5>=
< 19 33822862 * -A/* 131 131 47 13 -A * 1 12 0 0 0
< 19 33823047 S G 63 63 28 23 GggCggggggGgGGGGGgGGGGg A?B%BC@@7@?AAC7>?>@BBB8
< 19 33823417 A T 57 96 25 25 TTTTtTTtTtttttTtTtTtt.t.T 7;;<B@<B;A<CC>AB>A;@>B.>>
< 19 33834750 * */-A 89 89 46 11 * -A 7 4 0 0 0
< 19 33835435 * */+A 16 16 54 9 * +A 8 1 0 0 0
< 19 33836632 * */+CG 33 33 57 18 * +CG 17 1 0 0 0
< 19 33839207 Y C 47 47 27 21 cCCCCCccCcTcCTcCCcCCc ?4?3<*>?;?79=:=C?=>?%
---
> 19 33778072 T TT 63 0 42 12 ,,,..,,.,,.. >?<8>=?=,5@@

[lh3]

It is good to see the issue has been resolved. Thanks.