Extract column by name from another column split by separator using AWK

extract_subcolumn_info_awk

# We have a file that has a column with multiple additional "subcolumns" separated by the ; character
# We want to extract a specific subcolumn from the "merged" column that starts with a specific word

# Get 1000 Genomes project VCF
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/supporting/GRCh38_positions/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz

# This VCF has a INFO column (column no. 8) that stores additonal information
zcat ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz | grep -v "^#"| cut -f8 | head
#AC=35;AF=0.00698882;AFR_AF=0;AMR_AF=0.0072;AN=5008;CS=ALU_umary;EAS_AF=0.0069;EUR_AF=0.0189;MEINFO=AluYa4_5,1,223,-;NS=2504;SAS_AF=0.0041;SITEPOST=0.9998;SVLEN=222;SVTYPE=ALU;TSD=null
#AC=64;AF=0.0127795;AFR_AF=0.0015;AMR_AF=0;AN=5008;CIEND=-150,150;CIPOS=-150,150;CS=DUP_delly;EAS_AF=0.0595;END=914824;EUR_AF=0.001;IMPRECISE;NS=2504;SAS_AF=0.001;SITEPOST=1;SVTYPE=DUP
#AC=3,206;AF=0.00059904,0.0411342;AFR_AF=0,0.0303;AMR_AF=0.0014,0.0259;AN=5008;CS=DUP_gs;EAS_AF=0.001,0.0615;END=820586;EUR_AF=0.001,0.0417;NS=2504;SAS_AF=0,0.045;SITEPOST=1;SVTYPE=CNV
#AC=1;AF=0.00019968;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=0,354;CIPOS=-348,0;CS=DEL_union;EAS_AF=0.001;END=806640;EUR_AF=0;MC=BI_GS_DEL1_B4_P0001_3;NS=2504;SAS_AF=0;SVTYPE=DEL
#AC=188;AF=0.0375399;AFR_AF=0.0151;AMR_AF=0.062;AN=5008;CIEND=0,403;CIPOS=-385,0;CS=DEL_union;EAS_AF=0.0923;END=833732;EUR_AF=0.001;MC=EM_DL_DEL00011,YL_CN_CDX_8,BI_GS_DEL1_B1_P0001_18,SI_BD_2;NS=2504;SAS_AF=0.0317;SVTYPE=DEL

# As you can see, this column has many "subcolumns" separate by ";"; each of the subcolumn starts with some prefix (~name)
# These names are not on the same position for all the rows
# To get only subcolumn starting with "SVTYPE=", you can use AWK
zcat ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz | cut -f8 \
    | awk -F";" '{for(j=1;j<=NF;j++){if($j~/^SVTYPE+/){print $j}}}'

# You can also combine it with sort | uniq -c to get number of subcolumns with the same values
zcat ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz | cut -f8 \
    | awk -F";" '{for(j=1;j<=NF;j++){if($j~/^SVTYPE+/){print $j}}}' | sort | uniq -c
#  12743 SVTYPE=ALU
#   2899 SVTYPE=CNV
#  40922 SVTYPE=DEL
#   1231 SVTYPE=DEL_ALU
#      1 SVTYPE=DEL_HERV
#     56 SVTYPE=DEL_LINE1
#      9 SVTYPE=DEL_SVA
#   6006 SVTYPE=DUP
#    162 SVTYPE=INS
#    786 SVTYPE=INV
#   3047 SVTYPE=LINE1
#    835 SVTYPE=SVA

# You can also do this with a variable (and sort it)
field="SVTYPE"
zcat ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz | cut -f8 \
    | awk -F";" '{for(j=1;j<=NF;j++){if($j~/^'$field'+/){print $j}}}' | awk -F"=" '{print $2}' | sort | uniq -c | sort -k1,1r
#  40922 DEL
#  12743 ALU
#   6006 DUP
#   3047 LINE1
#   2899 CNV
#   1231 DEL_ALU
#    835 SVA
#    786 INV
#    162 INS
#     56 DEL_LINE1
#      9 DEL_SVA
#      1 DEL_HERV