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Scripts PanCancer Specific
Keiran Raine edited this page Jun 9, 2014
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These scripts are only relevant for users who are members of the ICGC/TCGA PanCancer working groups.
Generates submission XML files required to submit data to the PanCancer GNOS instances. Details of how to prepare your BAM/FASTQ data can be found on the OICR-PanCancer Wiki (requires login).
Regenerates *.bas file from analysisFull.xml URI. PCAP::Bam::Stats is able to parse this correctly regardless column ordering (which may be inconsistent).
e.g.
$: xml_to_bas.pl -d https://gtrepo-ebi.annailabs.com/cghub/metadata/analysisFull/4e183691-ba1f-4103-a517-948f363928b8
read_group_id #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_duplicate_reads #_gc_bases_r1 #_gc_bases_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_mapped_reads #_mapped_reads_properly_paired #_mapped_reads_r1 #_mapped_reads_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 bam_filename insert_size_sd library mean_insert_size median_insert_size platform platform_unit read_length_r1 read_length_r2 readgroup sample
WTSI25941 109656822 53400157 56256665 0 4900621926 4913073665 23957071382 12092611993 11864459389 242992645 91741465 121667967 121324678 243357940 121678970 121678970 out_4.bam 83.731 WGS:WTSI:12490 408.841 400.000 ILLUMINA WTSI:7119_5 100 100 WTSI25941 f8467ec8-2d5e-ba21-e040-11ac0c483584
WTSI25938 105448163 50962194 54485969 0 5059285020 5071727818 24756788121 12492499609 12264288512 251054082 94753203 125696465 125357617 251410540 125705270 125705270 out_1.bam 83.591 WGS:WTSI:12490 409.087 400.000 ILLUMINA WTSI:7119_2 100 100 WTSI25938 f8467ec8-2d5e-ba21-e040-11ac0c483584
WTSI25937 124757189 68266593 56490596 0 5003807799 5007016723 24418124464 12326534108 12091590356 247931492 93471492 124212116 123719376 248447342 124223671 124223671 out_0.bam 83.328 WGS:WTSI:12490 408.817 400.000 ILLUMINA WTSI:7119_1 100 100 WTSI25937 f8467ec8-2d5e-ba21-e040-11ac0c483584
WTSI25940 120711275 58333598 62377677 0 4926375001 4938756287 24057793106 12144140521 11913652585 244147184 92150919 122241408 121905776 244501826 122250913 122250913 out_3.bam 83.724 WGS:WTSI:12490 408.665 400.000 ILLUMINA WTSI:7119_4 100 100 WTSI25940 f8467ec8-2d5e-ba21-e040-11ac0c483584
WTSI25939 110785952 52341213 58444739 0 5110036344 5124651899 24997394847 12618022324 12379372523 253555020 95683446 126945749 126609271 253911232 126955616 126955616 out_2.bam 83.557 WGS:WTSI:12490 408.982 400.000 ILLUMINA WTSI:7119_3 100 100 WTSI25939 f8467ec8-2d5e-ba21-e040-11ac0c483584