What program(s) made these output files?

[lanzz]

I am searching a tool which can convert SOAPsnp(format) to vcf.

Does anyone know that?

[gringer]

We've recently had a 2GS carried out by an external facility, and they did some basic variation analysis on it. I would like to interpret this analysis, but don't know what program was used to generate it (and therefore don't know what all the columns mean). The facility produced documentation for one output format (SOAPsnp), but not the others shown below:

==> CNV/alts_M_C_L.anno.variant_function <==
intergenic      TUBB8(dist=23823),ZMYND11(dist=57205)   chr10   119001  123200  0       0       Copyratio:0.51412818168789      CNVlength:4200  BinNumber:6
intronic        DIP2C   chr10   522901  525000  0       0       Copyratio:0.0681283935965505    CNVlength:2100  BinNumber:3

==> CNV/alts_M_C_L.dat <==
chr10   119001  123200  6       0.51412818168789
chr10   522901  525000  3       0.0681283935965505

==> INDEL/1T.filter.vcf <==
##fileformat=VCFv4.1
##samtoolsVersion=0.1.16 (r963:234)

==> INDEL/1T.format.variant_function <==
intergenic      NONE(dist=NONE),TUBB8(dist=19917)       chr10   72911   72911   -       AAAA    hom     55.9    15      INDEL;DP=15;AF1=1;CI95=0.5,1;DP4=0,0,4,3;MQ=37;FQ=-47.5 GT:PL:GQ 1/1:133,50,37,95,0,89,122,31,79,119:23
upstream        TUBB8   chr10   95429   95429   -       A       het     191     38      INDEL;DP=38;AF1=0.5;CI95=0.5,0.5;DP4=6,9,14,7;MQ=48;FQ=194;PV4=0.18,1,2.5e-09,1 GT:PL:GQ        0/1:229,0,245:99

==> SV/1T.filter.gff <==
chr:10  INS     352698  352751  intron  NM_014974       334362  355969
chr:10  INS     490952  491074  intron  NM_014974       486937  518377

==> SV/1T.filter.sv <==
chr10   INS     365     44      155372  155373  2
chr10   INS     367     37      352698  352751  2

Any ideas what program(s) were used to generate these results?

Here's my current guess at columns:

1. CNV/alts_M_C_L.anno.variant_function: ?possibly ANNOVAR
2. CNV/alts_M_C_L.dat: chromosome, start position, end position, ?copy number, ?reliability
3. INDEL/1T.filter.vcf: VCF 1.4
4. INDEL/1T.format.variant_function: ?possibly ANNOVAR
5. SV/1T.filter.gff: GFF format, but does't seem to provide as much information as the .sv file
6. SV/1T.filter.sv: chromosome, variant type, ?, ?, start position, end position, ?variant count