||
AW pipeline 包含很多用的tools,比如利用VCF mask reference,比如split fasta文件,trimm fastq以及生产包含所有样本的qc文件等等吧,流程非常简洁,只有一下几个命令,根据自己的具体情况,修改相应的参数就可以。
scripts/GSmask.pl -i genome/ -v variants/chr19.exon.snps.vcf #mask ref
scripts/QC.sh -d reads #pre qc-test
scripts/Trim.pl -d reads -p -P "HEADCROP:5 LEADING:30 TRAILING:30 MINLEN:90" #trimm
scripts/QC.sh -d TRIM/Results #post qc-test
scripts/Align.pl -g GSMASK/Results -r TRIM/Results -p -a annotation/chr19.gtf -t 10 #aln
scripts/snpASE.pl -i TOPHAT/Results -v variants/chr19.exon.snps.vcf #snpASE
这一步可以用GATK完成
java -jar GenomeAnalysisTK.jar
-R reference.fasta
-T ASEReadCounter
-o file_name.csv
-I input.bam
-sites sites.vcf
-U ALLOW_N_CIGAR_READS
[-minDepth 10]
[--minMappingQuality 10]
[--minBaseQuality 2]
[-drf DuplicateRead]
scripts/transASE.pl -r transcripts/ntRef.fa -a transcripts/ntAlt.fa -p -i TRIM/Results #
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