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---
bamstats:
percentage_mapped_reads: "perl -nae 'if($_=~/percentage mapped reads:\\s+(\\S+)/) {print $1;last}' "
raw_total_sequences: "perl -nae 'if($_=~/raw total sequences:\\s+(\\S+)/) {print $1;last}' "
reads_mapped: "perl -nae 'if($_=~/reads mapped:\\s+(\\S+)/) {print $1;last}' "
bcftools:
version: "perl -nae 'if($_=~/bcftools_\\w+Version=(\\S+)/) {print $1;last;}' "
bwa:
version: "perl -nae 'if($_=~/\\[main\\]\\sVersion:\\s(\\S+)/) {print $1;last;}' "
chanjo:
version: "perl -nae 'if($_=~/version\\s(\\d+.\\d+.\\d+)/) {print $1;last;}' "
chanjo_sexcheck:
gender: "perl -nae 'if( ($F[0]!~/^#/) && ($F[2] =~/\\S+/) ) {print $F[2];}' "
collecthsmetrics:
header_info:
data: "perl -nae' if ( ($. ==8) && ($_ =~/(\\S+)/) ) {print $_;last;}' "
header: "perl -nae' if ($_ =~/^BAIT_SET/ ) {print $_;last;}' "
collectmultiplemetrics:
header_info:
first_of_pair: "perl -nae' if ($_ =~/^FIRST_OF_PAIR/ ) {print $_;last;}' "
header: "perl -nae' if ($_ =~/^CATEGORY/ ) {print $_;last;}' "
pair: "perl -nae' if ($_ =~/^PAIR/ ) {print $_;last;}' "
second_of_pair: "perl -nae' if ($_ =~/^SECOND_OF_PAIR/ ) {print $_;last;}' "
collectmultiplemetricsinsertsize:
header_info:
data: "perl -nae' if ( ($. ==8) && ($_ =~/(\\S+)/) ) {print $_;last;}' "
header: "perl -nae' if ($_ =~/^MEDIAN_INSERT_SIZE/ ) {print $_;last;}' "
delly:
version: "perl -nae 'if($_=~/SVMETHOD=EMBL\\.DELLY(v\\d+\\.\\d+\\.\\d+)/) {print $1;last }' "
fastqc:
basic_statistics: "perl -nae' if ($_=~/>>Basic Statistics\\s+(\\S+)/) {print $1;last;}' "
encoding: "perl -nae' if ($_=~/Encoding\\s+(\\S+\\s\\S+\\s\\S+\\s\\S+|\\S+\\s\\S+)/) { my $encoding = $1;$encoding=~s/\\s/\\_/g; print $encoding;last;}' "
gc: "perl -nae' if ($_=~/%GC\\s(\\d+)/) {print $1;last;}' "
kmer_content: "perl -nae' if ($_=~/>>Kmer Content\\s+(\\S+)/) {print $1;last;}' "
overrepresented_sequences: "perl -nae' if ($_=~/>>Overrepresented sequences\\s+(\\S+)/) {print $1;last;}' "
per_base_gc_content: "perl -nae' if ($_=~/>>Per base GC content\\s+(\\S+)/) {print $1;last;}' "
per_base_n_content: "perl -nae' if ($_=~/>>Per base N content\\s+(\\S+)/) {print $1;last;}' "
per_base_sequence_content: "perl -nae' if ($_=~/>>Per base sequence content\\s+(\\S+)/) {print $1;last;}' "
per_base_sequence_quality: "perl -nae' if ($_=~/>>Per base sequence quality\\s+(\\S+)/) {print $1;last;}' "
per_sequence_gc_content: "perl -nae' if ($_=~/>>Per sequence GC content\\s+(\\S+)/) {print $1;last;}' "
per_sequence_quality_scores: "perl -nae' if ($_=~/>>Per sequence quality scores\\s+(\\S+)/) {print $1;last;}' "
sequence_duplication: "perl -nae' if ($_=~/#Total Duplicate Percentage\\s+(\\d+.\\d)/) {print $1;last;}' "
sequence_duplication_levels: "perl -nae' if ($_=~/>>Sequence Duplication Levels\\s+(\\S+)/) {print $1;last;}' "
sequence_length: "perl -nae' if ($_=~/Sequence length\\s(\\d+)/) {print $1;last;}' "
total_number_of_reads: "perl -nae' if ($_=~/Total Sequences\\s(\\d+)/) {print $1;last;}' "
version: "perl -nae' if ($_=~/##FastQC\\s+(\\S+)/) {print $1;last;}' "
freebayes:
version: "perl -nae 'if($_=~/source=freeBayes\\s(\\S+)/) {print $1;last;}' "
genmod:
version: "perl -nae 'if($_=~/##Software=<ID=genmod,Version=(\\d+.\\d+.\\d+|\\d+.\\d+)/) {print $1;last;}' "
inbreeding_factor:
sample_inbreeding_factor: "perl -nae 'my @inbreedingFactor; if ($. > 1) {my @temp = split(/\\s/,$_);push(@inbreedingFactor, $F[0].\":\".$F[5]); print $inbreedingFactor[0], \"\\t\"; }' "
manta:
version: "perl -nae 'if($_=~/GenerateSVCandidates\\s+(\\S+)/) {print $1;last}' "
markduplicates:
fraction_duplicates: "perl -nae 'if($_=~/Fraction Duplicates\\: (\\S+)/) {print $1;}' "
pedigree_check:
sample_order: "perl -nae 'if ($_=~/^#CHROM/) {chomp $_; my @line = split(/\\t/,$_); for (my $sample=9;$sample<scalar(@line);$sample++) { print $line[$sample], \"\\t\";}last;}' "
plink2:
version: "perl -nae 'if($_=~/PLINK\\s(\\S+\\s\\S+\\s\\S+\\s\\S+\\s\\S+)/) {my $ret = $1;$ret =~s/\\s/_/g;print $ret;last;}' "
plink_sexcheck:
sample_sexcheck: "perl -nae 'my @sexCheckFactor; if ($. > 1) {my @temp = split(/\\s+/,$_);push(@sexCheckFactor,$temp[2].\":\".$temp[4]); print $sexCheckFactor[0], \"\\t\"; }' "
relation_check:
sample_relation_check: "perl -nae 'print $_;' "
samtools:
version: "perl -nae 'if($_=~/samtoolsVersion=(\\S+)/) {print $1;last;}' "
snpeff:
version: "perl -nae 'if($_=~/##SnpSiftVersion=\\\"(.+),/) {my $ret=$1; $ret=~s/\\s/_/g;print $ret;last;}' "
sv_combinevariantcallsets:
vcfanno: "perl -nae 'if($_=~/vcfanno\\sversion\\s(\\S+)/) {print $1;last;}' "
sv_genmod:
version: "perl -nae 'if($_=~/##Software=<ID=genmod,Version=(\\d+.\\d+.\\d+|\\d+.\\d+)/) {print $1;last;} else { if($_=~/#CHROM/) {last;} } ' "
sv_varianteffectpredictor:
assembly: "perl -nae 'if($_=~/##VEP=/ && $_=~/assembly=(\\S+)/) {print $1;last;}' "
cache: "perl -nae 'if($_=~/##VEP=\\w+\\s+cache=(\\S+)/) {print $1;last;}' "
gencode: "perl -nae 'if($_=~/##VEP=/ && $_=~/gencode=\\S+\\s+(\\d+)/) {print $1;last;}' "
gene_build: "perl -nae 'if($_=~/##VEP=/ && $_=~/genebuild=(\\S+)/) {print $1;last;}' "
hgmd_public: "perl -nae 'if($_=~/##VEP=/ && $_=~/HGMD-PUBLIC=(\\S+)/) {print $1;last;}' "
polyphen: "perl -nae 'if($_=~/##VEP=/ && $_=~/polyphen=(\\S+)/) {print $1;last;}' "
reg_build: "perl -nae 'if($_=~/##VEP=/ && $_=~/regbuild=(\\S+)/) {print $1;last;}' "
sift: "perl -nae 'if($_=~/##VEP=/ && $_=~/sift=sift(\\S+)/) {print $1;last;}' "
version: "perl -nae 'if($_=~/##VEP=(\\w+)/) {print $1;last;}' "
sv_vcfparser:
version: "perl -nae 'if($_=~/##Software=<ID=vcfParser.pl,Version=(\\d+.\\d+.\\d+)/) {print $1;last;} else { if($_=~/#CHROM/) {last;} }' "
svdb:
version: "perl -nae 'if($_=~/^##SVDB_version=(\\S+)/) { print $1; last; } else { if($_=~/#CHROM/) { last;} }' "
tiddit:
version: "perl -nae 'if($_=~/^##source=TIDDIT-(\\S+)/) { print $1; last; } else { if($_=~/#CHROM/) { last;} }' "
variant_integrity_father:
common_variants: "perl -nae 'unless ($_=~/^#/) {print $F[2];last;}' "
fraction_of_common_variants: "perl -nae 'unless ($_=~/^#/) {print $F[1];last;}' "
variant_integrity_mendel:
fraction_of_errors: "perl -nae 'unless ($_=~/^#/) {print $F[1];last;}' "
mendelian_errors: "perl -nae 'unless ($_=~/^#/) {print $F[2];last;}' "
varianteffectpredictor:
assembly: "perl -nae 'if($_=~/##VEP=/ && $_=~/assembly=(\\S+)/) {print $1;last;}' "
cache: "perl -nae 'if($_=~/##VEP=\\w+\\s+cache=(\\S+)/) {print $1;last;}' "
gencode: "perl -nae 'if($_=~/##VEP=/ && $_=~/gencode=\\S+\\s+(\\d+)/) {print $1;last;}' "
gene_build: "perl -nae 'if($_=~/##VEP=/ && $_=~/genebuild=(\\S+)/) {print $1;last;}' "
hgmd_public: "perl -nae 'if($_=~/##VEP=/ && $_=~/HGMD-PUBLIC=(\\S+)/) {print $1;last;}' "
polyphen: "perl -nae 'if($_=~/##VEP=/ && $_=~/polyphen=(\\S+)/) {print $1;last;}' "
reg_build: "perl -nae 'if($_=~/##VEP=/ && $_=~/regbuild=(\\S+)/) {print $1;last;}' "
sift: "perl -nae 'if($_=~/##VEP=/ && $_=~/sift=sift(\\S+)/) {print $1;last;}' "
version: "perl -nae 'if($_=~/##VEP=(\\w+)/) {print $1;last;}' "
variantevalall: &1
comp_overlap_header:
comp_overlap_data_all: "perl -nae' if ( ($_ =~/^CompOverlap/) && ($_ =~/all/) && ($_ =~/none/)) {print $_;last;}' "
comp_overlap_data_known: "perl -nae' if ( ($_ =~/^CompOverlap/) && ($_ =~/known\\s/) ) {print $_;last;}' "
comp_overlap_data_novel: "perl -nae' if ( ($_ =~/^CompOverlap/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
comp_overlap_header: "perl -nae' if ($_ =~/^CompOverlap\\s+CompRod/ ) {print $_;last;}' "
count_variants_header:
count_variants_data_all: "perl -nae' if ( ($_ =~/^CountVariants/) && ($_ =~/all\\s/) ) {print $_;last;}' "
count_variants_data_known: "perl -nae' if ( ($_ =~/^CountVariants/) && ($_ =~/known\\s/) ) {print $_;last;}' "
count_variants_data_novel: "perl -nae' if ( ($_ =~/^CountVariants/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
count_variants_header: "perl -nae' if ($_ =~/^CountVariants\\s+CompRod/ ) {print $_;last;}' "
indel_summary_header:
indel_summary_data_all: "perl -nae' if ( ($_ =~/^IndelSummary/) && ($_ =~/all\\s/) ) {print $_;last;}' "
indel_summary_data_known: "perl -nae' if ( ($_ =~/^IndelSummary/) && ($_ =~/known\\s/) ) {print $_;last;}' "
indel_summary_data_novel: "perl -nae' if ( ($_ =~/^IndelSummary/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
indel_summary_header: "perl -nae' if ($_ =~/^IndelSummary\\s+CompRod/ ) {print $_;last;}' "
multiallelic_summary_header:
multiallelic_summary_data_all: "perl -nae' if ( ($_ =~/^MultiallelicSummary/) && ($_ =~/all\\s/) ) {print $_;last;}' "
multiallelic_summary_data_known: "perl -nae' if ( ($_ =~/^MultiallelicSummary/) && ($_ =~/known\\s/) ) {print $_;last;}' "
multiallelic_summary_data_novel: "perl -nae' if ( ($_ =~/^MultiallelicSummary/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
multiallelic_summary_header: "perl -nae' if ($_ =~/^MultiallelicSummary\\s+CompRod/ ) {print $_;last;}' "
titv_variant_evaluator_header:
titv_variant_evaluator_data_all: "perl -nae' if ( ($_ =~/^TiTvVariantEvaluator/) && ($_ =~/all\\s/) ) {print $_;last;}' "
titv_variant_evaluator_data_known: "perl -nae' if ( ($_ =~/^TiTvVariantEvaluator/) && ($_ =~/known\\s/) ) {print $_;last;}' "
titv_variant_evaluator_data_novel: "perl -nae' if ( ($_ =~/^TiTvVariantEvaluator/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
titv_variant_evaluator_header: "perl -nae' if ($_ =~/^TiTvVariantEvaluator\\s+CompRod/ ) {print $_;last;}' "
validation_report_header:
validation_report_data_all: "perl -nae' if ( ($_ =~/^ValidationReport/) && ($_ =~/all\\s/) && ($_ =~/none\\s/)) {print $_;last;}' "
validation_report_data_known: "perl -nae' if ( ($_ =~/^ValidationReport/) && ($_ =~/known\\s/) ) {print $_;last;}' "
validation_report_data_novel: "perl -nae' if ( ($_ =~/^ValidationReport/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
validation_report_header: "perl -nae' if ($_ =~/^ValidationReport\\s+CompRod/ ) {print $_;last;}' "
variant_summary_header:
variant_summary_data_all: "perl -nae' if ( ($_ =~/^VariantSummary/) && ($_ =~/all\\s/) ) {print $_;last;}' "
variant_summary_data_known: "perl -nae' if ( ($_ =~/^VariantSummary/) && ($_ =~/known\\s/) ) {print $_;last;}' "
variant_summary_data_novel: "perl -nae' if ( ($_ =~/^VariantSummary/) && ($_ =~/novel\\s/) ) {print $_;last;}' "
variant_summary_header: "perl -nae' if ($_ =~/^VariantSummary\\s+CompRod/ ) {print $_;last;}' "
variantevalexome: *1
vcf2cytosure_version:
version: "perl -nae 'if($_=~/cytosure\\s+(\\d+[.]\\d+[.]\\d+)/xsm) { print $1;last; }' "
vcfparser:
version: "perl -nae 'if($_=~/##Software=<ID=vcfParser.pl,Version=(\\d+.\\d+.\\d+)/) {print $1;last;}' "
vt:
version: "perl -nae 'if($_=~/decompose\\sv(\\S+)/) {print $1;last;}' "