Angel's questions

我有一堆带有 .vcf 后缀的文件，逗号分隔并包含“，如下所示

"","CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT","NORMAL","TUMOR","Depth","DistanceToAlignmentEnd","DistanceToAlignmentEndMAD","DistanceToAlignmentEndMedian","HomopolymerLength","LowMapQual","MMQSDiff","MapQualDiff","MapQualDiffMedian","NT","QSS","QSS_NT","ReadCount","ReadCountControl","Repeat","SGT","SNVCluster10","SNVCluster100","SNVCluster20","SNVCluster5","SNVCluster50","SOMATIC","StrandBias","TQSS","TQSS_NT","VariantAlleleCount","VariantAlleleCountControl","VariantAlleleFrequency","VariantBaseQual","VariantBaseQualMedian","VariantMMQS","VariantMapQual","VariantMapQualMedian","VariantStrandBias","normal","tumour","N_DP","N_FDP","N_SDP","N_SUBDP","T_DP","T_FDP","T_SDP","T_SUBDP","T_REF_COUNT","T_ALT_COUNT","N_REF_COUNT","N_ALT_COUNT","T_VAF","N_VAF","N_AU_1","N_AU_2","N_CU_1","N_CU_2","N_GU_1","N_GU_2","N_TU_1","N_TU_2","T_AU_1","T_AU_2","T_CU_1","T_CU_2","T_GU_1","T_GU_2","T_TU_1","T_TU_2"
"1","chr1","11195689",".","C","G",".","PASS","Depth=83;DistanceToAlignmentEnd=38.75;DistanceToAlignmentEndMAD=9.00;DistanceToAlignmentEndMedian=37.50;HomopolymerLength=2;LowMapQual=0.00;MMQSDiff=136.94;MapQualDiff=-8.750e-01;MapQualDiffMedian=0.00;NT=ref;QSS=16;QSS_NT=16;ReadCount=83;ReadCountControl=49;Repeat=0;SGT=CC->CG;SNVCluster10=0;SNVCluster100=2;SNVCluster20=1;SNVCluster5=0;SNVCluster50=2;SOMATIC;StrandBias=0.482;TQSS=1;TQSS_NT=1;VariantAlleleCount=4;VariantAlleleCountControl=1;VariantAlleleFrequency=0.048;VariantBaseQual=40.00;VariantBaseQualMedian=41.00;VariantMMQS=157.25;VariantMapQual=59.00;VariantMapQualMedian=60.00;VariantStrandBias=0.250","DP:FDP:SDP:SUBDP:AU:CU:GU:TU","49:1:0:0:0,0:47,48:1,1:0,0","82:0:0:0:0,0:78,79:4,4:0,0","83","38.75","9","37.5","2","0","136.94","-0.875","0","ref","16","16","83","49","0","CC->CG","0","2","1","0","2","SOMATIC","0.482","1","1","4","1","0.048","40","41","157.25","59","60","0.25","list(DP = ""49"", FDP = ""1"", SDP = ""0"", SUBDP = ""0"", AU = ""0,0"", CU = ""47,48"", GU = ""1,1"", TU = ""0,0"")","list(DP = ""82"", FDP = ""0"", SDP = ""0"", SUBDP = ""0"", AU = ""0,0"", CU = ""78,79"", GU = ""4,4"", TU = ""0,0"")","49","1","0","0","82","0","0","0","78","4","47","1","0.0487804878048781","0.0208333333333333","0","0","47","48","1","1","0","0","0","0","78","79","4","4","0","0"

如何将逗号空间转换为制表符，删除“，删除第一列，最后将清理后的文件保存为 .txt，并使用匹配的原始文件的基本名称？

在一个文件夹中有一组匹配的文件，每对文件的名称是这样的，带有一个基本名称，例如

LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf.parsed.txt

和

LP6005334-DNA_H01_vs_LP6005333-DNA_H01.passed.somatic.indels.vcf_fixed_vcf.txt.hg19_multianno.txt

我如何columns 5th and 6th从文件passed.somatic.indels.vcf.parsed名中提取文件并将这些列附加到匹配的文件 ( ) 中，返回带有基本名称( )passed.somatic.indels.vcf_fixed_vcf.txt.hg19_multianno的输出.txtLP6005334-DNA_H01_vs_LP6005333-DNA_H01

为了切割我所做的列

[

fi1d18@cyan01 folder]$ for f in *.passed.somatic.indels.vcf.parsed.txt; do awk '{print $5,$6}' $f > $out
> done;
-bash: $out: ambiguous redirect

此后我不知道如何找到匹配的查找并将剪切列附加到

这是一对这些文件的链接

https://www.dropbox.com/s/y4jx1rznswqz6dq/LP6008460-DNA_G03_vs_LP6008340-DNA_C05__pv.1.7__rg.grch37_g1k__al.bwa_mem__.passed.somatic.indels.vcf_fixed_vcf.txt.hg19_multianno.txt?dl=0

和

我有一个 bash 脚本从 .vcf 文件中提取一些信息。如何更改此脚本以处理大量 .vcf 文件，同时为每个文件返回单独的 .txt 输出？

这是我的脚本

#!/usr/bash

#outfilename
outname=$(echo $1".parsed.txt")

#Header for output file
echo -e "Chrom"'\t'"Position"'\t'"Ref"'\t'"Alt"'\t'"TumorReadCount"'\t'"TumorVariantAlleleCount"'\t'"TumorReferenceAlleleCount"'\t'"NormalReadCount"'\t'"NormalVariantAlleleCount"'\t'"NormalReferenceAlleleCount"'\t'"VAF" > $outname

while read -r line ; 
do;

#Basic information
chrom=$(echo $line | sed 's/ /\t/g' | cut -f 1) #&& echo $chrom;
Pos=$(echo $line | sed 's/ /\t/g' |  cut -f 2) #&& echo $Pos;
Ref=$(echo $line | sed 's/ /\t/g' | cut -f 4)
Alt=$(echo $line | sed 's/ /\t/g' | cut -f 5)

#Tumor sample read, variant and reference information
ReadCount=$(echo $line | cut -f 8 | sed 's/;/\t/g' | cut -f 13 | sed 's/ReadCount=//' )
VariantAlleleCount=$(echo $line | cut -f 8 | sed 's/;/\t/g' | cut -f 26| sed 's/VariantAlleleCount=//')
ReferenceAlleleCount=$(echo $ line | awk -v rc=$ReadCount -v vac=$VariantAlleleCount '{print rc-vac}')


#Control or Normal read, variant, reference information
ReadCountControl=$(echo $line | cut -f 8 | sed 's/;/\t/g' | cut -f 14 | sed 's/ReadCountControl=//')
VariantAlleleCountControl=$(echo $line | cut -f 8 | sed 's/;/\t/g' | cut -f 27 | sed 's/VariantAlleleCountControl=//')   

ReferenceAlleleCountControl=$(echo $line | awk -v rcc=$ReadCountControl -v vacc=$VariantAlleleCountControl '{print rcc-vacc}')


VAF=$(echo $line | cut -f 8 | sed 's/;/\t/g' | cut -f 28 | sed 's/VariantAlleleFrequency=//')
#Print output
echo -e $chrom'\t'$Pos'\t'$Ref'\t'$Alt'\t'$ReadCount'\t'$VariantAlleleCount'\t'$ReferenceAlleleCount'\t'$ReadCountControl'\t'$VariantAlleleCountControl'\t'$ReferenceAlleleCountControl'\t'$VAF >> $outname ;

#Remove info tags from VCF
done; < <( egrep -v '#' $1)

当我添加for f in *.vcf退货时

[fi1d18@cyan01 snp]$ bash vcf_parasing.sh
vcf_parasing.sh: line 7: syntax error near unexpected token `echo'
vcf_parasing.sh: line 7: `echo -e "Chrom"'\t'"Position"'\t'"Ref"'\t'dCount"'\t'"TumorVariantAlleleCount"'\t'"TumorReferenceAlleleCount"'\t'"NormalRelVariantAlleleCount"'\t'"NormalReferenceAlleleCount"'\t'"VAF" > $outname'