User:Lindenb/Notebook/UMR915/2012/03/05: Difference between revisions
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"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." | "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." | ||
TODO: add the path to samtools in the exomeCNV tools. | |||
Revision as of 07:35, 5 March 2012
 Project name
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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."
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