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Help generating a script for next-generation sequencing data
11-23-2011
echo Please enter family number read FALS OUT=”$FALS_affected_variants.txt” (is this correct?) echo “The output file is $OUT” echo Please enter number of affected samples in family read ?
echo Please enter affected sample 1 read AFF1 echo Please enter affected sample 2 read AFF2 echo Please enter affected sample 3 read AFF3 echo Please enter affected sample 4 read AFF4
.A393T) in each line (one line at a time) in the $FALS_affected_variants.txt file to the “control” .txt files. If the data in column 15 from $FALS_affected_variants.txt is present in ANY of the “control” .txt files, I want to add an extra column to $FALS_affected_variants.txt (a 20th column with heading in_controls) with the word “yes”, or if it is NOT present in any of the “control” .txt files, the word “no” added to column 20. Or, if it is easier, generate a new output file $FALS_affected_variants_with_control_data.txt with the same 19 columns from the original $FALS_affected_variants.txt with a new 20th column "in_controls" with "yes" or "no"chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq chr01 11298631 11298631 G A het 85 38 20 . . exonic MTOR synonymous SNV MTOR:NM_004958:exon12:c.C1830T:p.F610F, . . . chr01 11589817 11589817 C T het 54 15 9 . . intronic PTCHD2 . . . . . chr01 12908349 12908349 - T het 1835 128 54 . . intronic HNRNPCL1 . . . . . chr01 12921386 12921386 G A het 228 170 75 . . exonic PRAMEF2 nonsynonymous SNV PRAMEF2:NM_023014:exon4:c.G1177A:p.A393T, . 1000g2010nov_all 0.008 chr01 12939546 12939546 - G het 1535 157 50 . . exonic PRAMEF4 frameshift insertion PRAMEF4:NM_001009611:exon4:c.1256_1257insC:p.R419fs, . . . chr01 12939568 12939568 C G het 48 159 52 . . exonic PRAMEF4 nonsynonymous SNV PRAMEF4:NM_001009611:exon4:c.G1234C:p.V412L, . . . chr01 12954490 12954490 A G het 128 74 35 . . exonic PRAMEF10 nonsynonymous SNV PRAMEF10:NM_001039361:exon3:c.T793C:p.C265R, . 1000g2010nov_all 0.065
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq chr01 12834987 12834987 - T het 683 53 22 . . UTR5 PRAMEF12 . . . . . chr01 12908349 12908349 - T het 1943 153 61 . . intronic HNRNPCL1 . . . . . chr01 12921386 12921386 G A het 228 234 119 . . exonic PRAMEF2 nonsynonymous SNV PRAMEF2:NM_023014:exon4:c.G1177A:p.A393T, . 1000g2010nov_all 0.008 chr01 12939546 12939546 - G het 3903 397 118 . . exonic PRAMEF4 frameshift insertion PRAMEF4:NM_001009611:exon4:c.1256_1257insC:p.R419fs, . . . chr01 12939568 12939568 C G het 55 344 120 . . exonic PRAMEF4 nonsynonymous SNV PRAMEF4:NM_001009611:exon4:c.G1234C:p.V412L, . . .
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq chr01 12041977 12041977 - T het 64 6 3 snp131 rs34602102 intronic MFN2 . . . . . chr01 12267373 12267373 G T het 22 6 2 . . UTR3 TNFRSF1B . . . . . chr01 12268023 12268023 - AA het 1278 46 1 . . UTR3 TNFRSF1B . . . . . chr01 12368706 12368706 T - het 83 15 3 . . intronic VPS13D . . . . . chr01 12677725 12677725 A - het 157 29 5 . . UTR5 DHRS3 . . . . . chr01 12908349 12908349 - T het 841 57 24 . . intronic HNRNPCL1 . . . . . chr01 12921386 12921386 G A het 228 170 75 . . exonic PRAMEF2 nonsynonymous SNV PRAMEF2:NM_023014:exon4:c.G1177A:p.A393T, . 1000g2010nov_all 0.008 chr01 12939546 12939546 - G het 1535 157 50 . . exonic PRAMEF4 frameshift insertion PRAMEF4:NM_001009611:exon4:c.1256_1257insC:p.R419fs, . . .
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq chr01 12035057 12035057 - G het 20 33 1 . . UTR3 PLOD1 . . . . . chr01 12254746 12254746 - A het 128 10 3 . . intronic TNFRSF1B . . . . . chr01 12268023 12268023 - TGAA hom 1661 24 22 . . UTR3 TNFRSF1B . . . . . chr01 12677725 12677725 A - het 50 10 2 . . UTR5 DHRS3 . . . . . chr01 12908349 12908349 - T het 643 53 21 . . intronic HNRNPCL1 . . . . . chr01 12921386 12921386 G A het 228 170 75 . . exonic PRAMEF2 nonsynonymous SNV PRAMEF2:NM_023014:exon4:c.G1177A:p.A393T, . 1000g2010nov_all 0.008
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq subjects chr01 12921386 12921386 G A het 228 170 75 . . exonic PRAMEF2 nonsynonymous SNV PRAMEF2:NM_023014:exon4:c.G1177A:p.A393T, . 1000g2010nov_all 0.008 3 chr01 12939546 12939546 - G het 1535 157 50 . . exonic PRAMEF4 frameshift insertion PRAMEF4:NM_001009611:exon4:c.1256_1257insC:p.R419fs, . . . 3 chr01 12939568 12939568 C G het 48 159 52 . . exonic PRAMEF4 nonsynonymous SNV PRAMEF4:NM_001009611:exon4:c.G1234C:p.V412L, . . . 2
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq subjects in_controls chr01 12921386 12921386 G A het 228 170 75 . . exonic PRAMEF2 nonsynonymous SNV PRAMEF2:NM_023014:exon4:c.G1177A:p.A393T, . 1000g2010nov_all 0.008 3 yes chr01 12939546 12939546 - G het 1535 157 50 . . exonic PRAMEF4 frameshift insertion PRAMEF4:NM_001009611:exon4:c.1256_1257insC:p.R419fs, . . . 3 no chr01 12939568 12939568 C G het 48 159 52 . . exonic PRAMEF4 nonsynonymous SNV PRAMEF4:NM_001009611:exon4:c.G1234C:p.V412L, . . . 2 no
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