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dnaase / Bis-tools

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )
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Malformed VCF output in snp.raw.vcf files #3

Open wac opened 5 years ago

wac commented 5 years ago

In both versions 1.0.0 and 1.0.1, I have been getting VCF lines that have 19 columns rather than the expected 10 columns, as well as blank links. It appears that some lines are concatenated together (where the chromosome of the subsequent line is concatenated with the subsequent line. I was running BisSNP in multithreaded mode with quite a few threads (usually 10 or 23) - it does look like something to do with the I/O. A couple examples follow:

This one has two malformed lines in a row that are also a duplicate of one another followed by a blank line

6       168841154       .       A       G       74.88   PASS    DP=16;MQ0=0;NS=1;SB=-0.0007     GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/1:35.9,NaN:0,0,2,0,0,14:.:.:.:.:2,14,0,0:75,0,76:75:56        167467433   rs1358883       G       C       54.53   PASS    CS=-;DB;DP=15;MQ0=0;NS=1;REF=C,CH;SB=-0.1779GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS     0/1:36.6,37.0:0,0,9,3,0,2:.:.:.:.:9,0,0,3:55,0,408:55:5
6       168841154       .       A       G       74.88   PASS    DP=16;MQ0=0;NS=1;SB=-0.0007     GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/1:35.9,NaN:0,0,2,0,0,14:.:.:.:.:2,14,0,0:75,0,76:75:56        167467433   rs1358883       G       C       54.53   PASS    CS=-;DB;DP=15;MQ0=0;NS=1;REF=C,CH;SB=-0.1779GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS     0/1:36.6,37.0:0,0,9,3,0,2:.:.:.:.:9,0,0,3:55,0,408:55:5

And another example with a malformed line followed by a correctly formatted line that duplicates part of the malformed line followed by a blank line

11      119559423       .       G       A       56.45   PASS    CS=-;DP=11;MQ0=0;NS=1;REF=C,CH;SB=-0.0000       GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS     0/1:35.5,35.7:0,0,11,0,0,0:.:.:.:.:8,0,3,0:56,0,292:56:511      118901796       .       T       C       33.69   PASS    DP=13;MQ0=0;NS=1;SB=-32.7049    GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS     0/1:37.0,37.0:0,7,0,2,4,0:.:.:.:.:7,4,0,2:34,0,152:34:5
11      119559423       .       G       A       56.45   PASS    CS=-;DP=11;MQ0=0;NS=1;REF=C,CH;SB=-0.0000       GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS     0/1:35.5,35.7:0,0,11,0,0,0:.:.:.:.:8,0,3,0:56,0,292:56:5

Also, this issue does not appear to occur in the older (0.82.2) so perhaps it is something in the interface with the new GATK?

YaliBai commented 5 years ago

I got the same question. The line with the wrong columns which seems likes two lines merged together. And the next line will be an empty line.

chr1    1186408 .   C   .   34.76   PASS    CS=+;Context=WCG;DP=1;MQ0=0;NS=1;REF=0  GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/0:38.0,NaN:1,0,0,0,0,0:1:WCG:0:.:1,0,0,0:0,35,78:35:5
chr1    1320899 .   G   .   37.77   PASS    CS=-;Context=GCH;DP=2;MQ0=0;NS=1;REF=0  GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/0:36.0,NaN:0,0,0,2,0,0:0:GCH:0:.:2,0,0,0:0,38,116:38:5chr1    1573517 31.75   PASS    CS=-;Context=HCH;DP=1;MQ0=0;NS=1;REF=0  GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/0:39.0:0,1,0,0,0,0:0:HCH:1:.:0,0,0,1:0,32,35:32:5

chr1    1320899 .   G   .   37.77   PASS    CS=-;Context=GCH;DP=2;MQ0=0;NS=1;REF=0  GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/0:36.0,NaN:0,0,0,2,0,0:0:GCH:0:.:2,0,0,0:0,38,116:38:5chr1    1573517 31.75   PASS    CS=-;Context=HCH;DP=1;MQ0=0;NS=1;REF=0  GT:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/0:39.0:0,1,0,0,0,0:0:HCH:1:.:0,0,0,1:0,32,35:32:5