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zhoulab / sclc-scripts

scripts for "Significantly mutated genes and regulatory pathways in SCLC—a meta-analysis"
https://doi.org/10.1016/j.cancergen.2017.05.003
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Transform VCF file #1

Closed victorlin closed 7 years ago

victorlin commented 7 years ago

Folder: ZhouLab_Folder/Projects/Oncogenomics/SCLC/Data/Umemura/Kouya Shiraishi - SCLC_vcf/SCLC_vcf

File: SCLC.muTect.vcf

Input

columns:

The samples (patients) containing a mutation in a specific position (each row) are depicted with a group of numbers like 0/1:25,8:30:33:0.242:2 and the rest are filled with ./.:.:.:.:.:.

Note: Ignore lines starting with ##

Output

SCLC.muTect.vcf

columns:

Example

Input:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  M153T   M189T   M288T   SM09_002T   SM09_016T   SM09-001T   SM09-003T   SM09-004T   SM09-005_tumor  SM09-006_tumor  SM09-007T   SM09-008T   SM09-010T   SM09-012T   SM09-013T   SM09-014T   SM09-015T   SM09-017_tumor  SM09-018_tumor  SM09-019_tumor  SM09-020_tumor  11169T  12878T  19100T  SBM_T04 SBM_T08 SBM_T17 SBM_T37 SBM_T40 THB_Lu_1T   THB_Lu_2T   THB_Lu_3T   THB_Lu_4T   THB_Lu_5T   1581M   1582M   1591T   1592M   1594M   1595M   1601T   1602M   SM09-011T1  SM09-011T2
chr1    14728   .   C   A   .   PASS    SOMATIC;VT=SNP;AC=2;AN=4    GT:AD:BQ:DP:FA:SS   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   ./.:.:.:.:.:.   0/1:30,20:29:50:0.4:2   0/1:56,25:28:81:0.309:2 ./.:.:.:.:.:.   ./.:.:.:.:.:.

Output:

chr   start  end   ref_allele alt_allele patient
chr1  14728  14728 C          A          1601T
chr1  14728  14728 C          A          1602M
victorlin commented 7 years ago

related: pandas.DataFrame manipulation on SO