`chromosome_strand` all change to `1`
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4.3 years ago
wangshx ▴ 10

The chromosome_strand column should indicate "-" or "+". It is right when I use zcat simple_somatic_mutation.open.tsv.gz |head -5 to see the head of data (from ICGC tsv file). But when I use awk to get some columns I am interested in, chromosome_strand all change to 1. Anybody know why?

  $zcat simple_somatic_mutation.open.tsv.gz |head -5 | awk 'BEGIN{FS="\t";OFS="\t";} {print $1,$2,$3,$12}'
    icgc_mutation_id    icgc_donor_id   project_code    chromosome_strand
    MU28469596  DO50633 BOCA-FR 1
    MU28469596  DO50633 BOCA-FR 1
    MU28469596  DO50633 BOCA-FR 1
    MU28469596  DO50633 BOCA-FR 1
ICGC awk • 871 views
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paste the output of zcat simple_somatic_mutation.open.tsv.gz |head -5

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 $zcat simple_somatic_mutation.open.tsv.gz |head -5
icgc_mutation_id    icgc_donor_id   project_code    icgc_specimen_id    icgc_sample_id  matched_icgc_sample_id  submitted_sample_id submitted_matched_sample_id chromosome  chromosome_start    chromosome_end  chromosome_strand   assembly_version    mutation_type   reference_genome_allelemutated_from_allele  mutated_to_allele   quality_score   probability total_read_count    mutant_allele_read_count    verification_status verification_platform   biological_validation_status    biological_validation_platform  consequence_type    aa_mutation cds_mutation    gene_affected   transcript_affected gene_build_version  platform    experimental_protocol   sequencing_strategy base_calling_algorithm  alignment_algorithm variation_calling_algorithm other_analysis_algorithm    seq_coverage    raw_data_repository raw_data_accession  initial_data_release_date
MU28469596  DO50633 BOCA-FR SP111595    SA529113    SA529110    IC280T_WGS  IC280C_WGS  X   123185046   123185046   1   GRCh37  deletion of <=200bp G   G   -           60  20  not tested      not tested      frameshift_variant  E365        ENSG00000101972 ENST00000371157 75  Illumina HiSeq  Paired-End http://technology.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html    WGS CASAVA http://support.illumina.com/sequencing/sequencing_software/casava.ilmn   BWA http://bio-bwa.sourceforge.net/bwa.shtml    Bambino https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html        35.0    EGA EGAS00001000855 
MU28469596  DO50633 BOCA-FR SP111595    SA529113    SA529110    IC280T_WGS  IC280C_WGS  X   123185046   123185046   1   GRCh37  deletion of <=200bp G   G   -           60  20  not tested      not tested      frameshift_variant  E365        ENSG00000101972 ENST00000371160 75  Illumina HiSeq  Paired-End http://technology.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html    WGS CASAVA http://support.illumina.com/sequencing/sequencing_software/casava.ilmn   BWA http://bio-bwa.sourceforge.net/bwa.shtml    Bambino https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html        35.0    EGA EGAS00001000855 
MU28469596  DO50633 BOCA-FR SP111595    SA529113    SA529110    IC280T_WGS  IC280C_WGS  X   123185046   123185046   1   GRCh37  deletion of <=200bp G   G   -           60  20  not tested      not tested      frameshift_variant  E365        ENSG00000101972 ENST00000371144 75  Illumina HiSeq  Paired-End http://technology.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html    WGS CASAVA http://support.illumina.com/sequencing/sequencing_software/casava.ilmn   BWA http://bio-bwa.sourceforge.net/bwa.shtml    Bambino https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html        35.0    EGA EGAS00001000855 
MU28469596  DO50633 BOCA-FR SP111595    SA529113    SA529110    IC280T_WGS  IC280C_WGS  X   123185046   123185046   1   GRCh37  deletion of <=200bp G   G   -           60  20  not tested      not tested      frameshift_variant  E365        ENSG00000101972 ENST00000455404 75  Illumina HiSeq  Paired-End http://technology.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html    WGS CASAVA http://support.illumina.com/sequencing/sequencing_software/casava.ilmn   BWA http://bio-bwa.sourceforge.net/bwa.shtml    Bambino https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html        35.0    EGA EGAS00001000855

............. too many columns. Thanks for reminding me. I am wrong~

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So your 12th col is not the strand, as you might have noticed too.

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