User:Lindenb/Notebook/UMR915/2012/03/05: Difference between revisions
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TODO: add the path to samtools in the exomeCNV tools. | TODO: add the path to samtools in the exomeCNV tools. | ||
updated GATK | |||
==Knime4bio== | |||
added two nodes for Knime4bio: read mpileup and smart numeric filtering: http://code.google.com/p/knime4bio/source/detail?r=220 | |||
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Revision as of 08:43, 5 March 2012
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DailyProject RPTransfert BAM to server: XXXX1.fastq.gz 100% 58GB 32.6MB/s 30:29 XXXX2.fastq.gz 100% 58GB 32.7MB/s 30:21 XXXXsorted.bam 100% 97GB 30.8MB/s 53:36 XXXXsorted.bam.bai 100% 8595KB 8.4MB/s 00:01 XXXX1.fastq.gz 100% 53GB 28.8MB/s 31:36 XXXX2.fastq.gz 100% 53GB 33.1MB/s 27:29 XXXXsorted.bam 100% 78GB 33.1MB/s 40:21 XXXXsorted.bam.bai 100% 8565KB 8.4MB/s 00:01 XXXX1.fastq.gz 100% 51GB 33.0MB/s 26:34 XXXX2.fastq.gz 100% 51GB 33.1MB/s 26:22 XXXXsorted.bam 100% 80GB 33.1MB/s 41:13 XXXXsorted.bam.bai 100% 8608KB 8.4MB/s 00:00 XXXX1.fastq.gz 100% 52GB 33.1MB/s 26:37 XXXX2.fastq.gz 100% 52GB 33.1MB/s 26:37 XXXXsorted.bam 100% 83GB 33.1MB/s 42:49 XXXXsorted.bam.bai 100% 8607KB 8.4MB/s 00:00 XXXX1.fastq.gz 100% 57GB 33.1MB/s 29:34 XXXX2.fastq.gz 100% 57GB 33.1MB/s 29:38 XXXXsorted.bam 100% 92GB 33.1MB/s 47:34 XXXXsorted.bam.bai 100% 8619KB 8.4MB/s 00:00 Test mpileup$ samtools mpileup -D -u -f hg19.fa DataHD20120302/*/*.bam | bcftools view -bvcg - | bcftools view - | grep -v "##" | head -n 3 | verticalize [mpileup] 5 samples in 5 input files <mpileup> Set max per-file depth to 1600 >>> 2 $1 #CHROM chr1 $2 POS 9997 $3 ID . $4 REF N $5 ALT A $6 QUAL 3.55 $7 FILTER . $8 INFO DP=1;AF1=1;AC1=10;DP4=0,0,1,0;MQ=60;FQ=-25.5 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 0/1:31,3,0:1:5 $11 DataHD20120302/CD8260/CD8260_sorted.bam 0/0:0,0,0:0:3 $12 DataHD20120302/CD8262/CD8262_sorted.bam 0/0:0,0,0:0:3 $13 DataHD20120302/CD8289/CD8289_sorted.bam 0/0:0,0,0:0:3 $14 DataHD20120302/S0529/S0529_sorted.bam 0/0:0,0,0:0:3 <<< 2 >>> 3 $1 #CHROM chr1 $2 POS 9998 $3 ID . $4 REF N $5 ALT C $6 QUAL 29 $7 FILTER . $8 INFO DP=2;AF1=1;AC1=10;DP4=0,0,2,0;MQ=60;FQ=-27.4 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 1/1:31,3,0:1:6 $11 DataHD20120302/CD8260/CD8260_sorted.bam 1/1:0,0,0:0:3 $12 DataHD20120302/CD8262/CD8262_sorted.bam 1/1:0,0,0:0:3 $13 DataHD20120302/CD8289/CD8289_sorted.bam 1/1:0,0,0:0:3 $14 DataHD20120302/S0529/S0529_sorted.bam 1/1:31,3,0:1:6 <<< 3 vs only one sample: $ samtools mpileup -D -u -f hg19.fa DataHD20120302/CD5121/CD5121_sorted.bam | bcftools view -bvcg - | bcftools view - | grep -v "##" | head -n 3 | verticalize [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 >>> 2 $1 #CHROM chr1 $2 POS 9997 $3 ID . $4 REF N $5 ALT A $6 QUAL 3.55 $7 FILTER . $8 INFO DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 0/1:31,3,0:1:4 <<< 2 >>> 3 $1 #CHROM chr1 $2 POS 9998 $3 ID . $4 REF N $5 ALT C $6 QUAL 3.55 $7 FILTER . $8 INFO DP=1;AF1=1;AC1=2;DP4=0,0,1,0;MQ=60;FQ=-30 $9 FORMAT GT:PL:DP:GQ $10 DataHD20120302/CD5121/CD5121_sorted.bam 0/1:31,3,0:1:4 <<< 3 exomeCNVreceived message from author "Thank you for your email. I fixed the problem and the script should be functional now. Please let me know if you notice anything else not working or if you have any question about ExomeCNV."
updated GATK Knime4bioadded two nodes for Knime4bio: read mpileup and smart numeric filtering: http://code.google.com/p/knime4bio/source/detail?r=220 |