Report LGC 170815

@RG     ID:D07MJ        PL:IONTORRENT   PU:PGM/900

WARNINGS

/media/raony/storage/received_exomes/5exomes/R_2014_03_14_12_01_11_user_PR6-64-KLF_Auto_user_PR6-64-KLF_90.bam
TAMANHO:54.6GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_14_12_01_11_user_PR6-64-KLF_Auto_user_PR6-64-KLF_90.bam.bai
ID:8TB8O
/media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_29_40_user_PR1-7-ACLF_Auto_user_PR1-7-ACLF_134.bam
TAMANHO:35.3GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_29_40_user_PR1-7-ACLF_Auto_user_PR1-7-ACLF_134.bam.bai
ID:R44KW
/media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_30_52_user_PR2-93-LGLF_Auto_user_PR2-93-LGLF_124.bam
TAMANHO:43.1GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_30_52_user_PR2-93-LGLF_Auto_user_PR2-93-LGLF_124.bam.bai
/media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_31_20_user_PR3-92-LEGF_Auto_user_PR3-92-LEGF_126.bam
TAMANHO:43.4GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/5exomes/R_2014_03_12_14_31_20_user_PR3-92-LEGF_Auto_user_PR3-92-LEGF_126.bam.bai
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/june_july_2014/MM140545/coverage_analysis_out/IonXpress_008_R_2014_06_10_15_13_57_user_PR3-131-SP_MM140545_CM_AT-1_Auto_user_PR3-131-SP_MM140545_CM_AT-1_166.bam.bai

/media/raony/storage/received_exomes/020715/Arquivos da Natália/VSS.bam
TAMANHO:15.5GiB
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/VSS.bai
ID:Q3ESQ.IonXpress_013
achou ampliseq
/media/raony/storage/received_exomes/020715/Arquivos da Natália/TYSS.bam
TAMANHO:21.1GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/TYSS.bai
ID:RV1P2.IonXpress_012
achou ampliseq
/media/raony/storage/received_exomes/020715/Arquivos da Natália/JPBS.bam
TAMANHO:21.4GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/JPBS.bai
ID:A7H2K.IonXpress_006
achou ampliseq
/media/raony/storage/received_exomes/020715/Arquivos da Natália/TRS.bam
TAMANHO:21.3GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/020715/Arquivos da Natália/TRS.bai
ID:RV1P2.IonXpress_011

/media/raony/storage/received_exomes/vcfmms2/PR2-40-mm13490.bam
TAMANHO:30.9GiB
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/vcfmms2/PR2-40-mm13490.bam.bai
ID:ND13A

/media/raony/storage/received_exomes/150515/MM150125MO.bam
TAMANHO:23.9GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/150515/MM150125MO.bam.bai
ID:QGLE1.IonXpress_015
achou ampliseq
/media/raony/storage/received_exomes/150515/MM150137LN.bam
TAMANHO:28.0GiB
Warning: The index file is older than the data file: /media/raony/storage/received_exomes/150515/MM150137LN.bam.bai
ID:QGLE1.IonXpress_016

/media/raony/storage/received_exomes/exomes070513/PR4-11-mm13174_13.bam
TAMANHO:31.1GiB
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
ID:IXZYA

cat human_g1k_v37.fasta | sed ‘s/>/>chr/g’ > human_g1k_v37chr.fasta

http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
java -Xmx40g -jar /home/raony/bin/gatk/GenomeAnalysisTK.jar -T DepthOfCoverage -I ampliseq.group2.list -L /home/raony/datasets/beds/AmpliSeqExome.20141113.designed_effective.bed -R /home/raony/datasets/b37/human_g1k_v37chr.fasta -dt BY_SAMPLE -dcov 5000 -l INFO –omitDepthOutputAtEachBase –omitLocusTable –minBaseQuality 0 –minMappingQuality 20 –start 1 –stop 5000 –nBins 200 –includeRefNSites –countType COUNT_FRAGMENTS -o group2.DATA
java -Xmx40g -jar /home/raony/bin/gatk/GenomeAnalysisTK.jar -T DepthOfCoverage -I ampliseq.group3.list -L /home/raony/datasets/beds/AmpliSeqExome.20141113.designed_effective.bed -R /home/raony/datasets/b37/human_g1k_v37chr.fasta -dt BY_SAMPLE -dcov 5000 -l INFO –omitDepthOutputAtEachBase –omitLocusTable –minBaseQuality 0 –minMappingQuality 20 –start 1 –stop 5000 –nBins 200 –includeRefNSites –countType COUNT_FRAGMENTS -o group3.DATA