Retrieve the finished Job by ID
Ion AmpliSeq™ Cancer Hotspot Panel: v1 (45 genes) v2 (50 genes)
Torrent Variant Caller (TVC): v3.2 (supported format .vcf or .xls) v3.6 (.xls only) v4.0 (.xls only) (new!)


Demonstration Datasets: test.tar.bz2, test.tar.gz, VCF.tar.bz2 and VCF.tar.gz

Step 1: Retrieve variant calling file ("variant.xls" or "TSVC_variants.vcf") from Torrent Server
The content of variant.xls
Chrom Position Gene Sym Target ID Type Zygosity Ref Variant Var Freq P-value Coverage Ref Cov Var Cov HotSpot ID
chr3 178936091 PIK3CA AMPL35831 SNP Het G A 54.82 1.26E-05 1795 811 984 COSM763;
chr3 178938877 PIK3CA AMPL339432 SNP Het G A 22.4 6.31E-05 433 336 97 ---
chr4 1806181 FGFR3 AMPL142574 SNP Hom C G 61.2 1.00E-07 317 122 194 ---
chr4 1807894 FGFR3 AMPL411633 SNP Hom G A 99.41 2.00E-09 1015 6 1009 ---
chr4 55141055 PDGFRA AMPL43181 SNP Hom A G 100 5.01E-09 797 0 797 ---
chr4 55962451 KDR AMPL52189 SNP Het A G 2.13 7.94E-05 1031 1008 22 ---
chr5 112175617 APC AMPL145156 SNP Het T A 67.47 5.01E-05 292 94 197 ---
chr5 112175770 APC AMPL59934 SNP Het G A 98.85 1.00E-03 2693 30 2662
chr7 55249063 EGFR AMPL493236 SNP Hom G A 99.53 1.58E-09 1070 3 1065 ---
chr10 43613843 RET AMPL78961 SNP Hom G T 100 2.00E-08 576 0 576 ---
chr14 105246407 AKT1 AMPL329410 SNP Hom G A 99.76 2.00E-10 1696 4 1692 ---
chr17 37881497 ERBB2 AMPL504796 SNP Het G A 1.44 2.51E-03 975 961 14 ---
The content of TSVC_variants.vcf (example)
Step 2: Rename variant calling files
Nomenclature Criteria
Sample_Barcode Redundant_Name Non-Redundant_Name
IonXpress_001 variant.xls or TSVC_variants.vcf Sample1.xls or Sample1.vcf
IonXpress_002 variant.xls or TSVC_variants.vcf Sample2.xls or Sample2.vcf
IonXpress_003 variant.xls or TSVC_variants.vcf Sample3.xls or Sample3.vcf
IonXpress_004 variant.xls or TSVC_variants.vcf Sample4.xls or Sample4.vcf
IonXpress_005 variant.xls or TSVC_variants.vcf Sample5.xls or Sample5.vcf
IonXpress_006 variant.xls or TSVC_variants.vcf Sample6.xls or Sample6.vcf
IonXpress_007 variant.xls or TSVC_variants.vcf Sample7.xls or Sample7.vcf
IonXpress_008 variant.xls or TSVC_variants.vcf Sample8.xls or Sample8.vcf
IonXpress_009 variant.xls or TSVC_variants.vcf Sample9.xls or Sample9.vcf
IonXpress_010 variant.xls or TSVC_variants.vcf Sample10.xls or Sample10.vcf
Step 3: Compress & Upload variant calling files
Supported format (tar.bz2, tar.gz and zip)
Variant calling files Single compressed file
Sample1.xls or Sample1.vcf
Sample2.xls or Sample2.vcf
Sample3.xls or Sample3.vcf
Sample4.xls or Sample4.vcf ( A mixture of *.xls and *.vcf is not allowed. )
Sample5.xls or Sample5.vcf upload.tar.bz2 or
Sample6.xls or Sample6.vcf upload.tar.gz or
Sample7.xls or Sample7.vcf upload.zip
Sample8.xls or Sample8.vcf
Sample9.xls or Sample9.vcf
Sample10.xls or Sample10.vcf