Hi all.
I want to use IGV for viewing my BAM file data which I generated by Hiseq2000.
Using ELANDv2, the data was aligned to hg18 and called SNP and small IN/DEL.
However, when I open the BAM file as output data of ELANDv2 on IGV, any data is not shown.
As searching the reason, I could find this suggestion - http://www.broadinstitute.org/softwa...ata/#aliasfile
So, I made the alias file and located the location that page mentioned.
But, the result is same with before.
Is anyone help me?
Below is my sample SAM data.
@HD VN:1.0 SO:coordinate
@PG ID:CASAVA VN:CASAVA-1.8.1 CL:/usr/local/bin/configureBuild.pl --id /illumina2/data/111020_SN336_0133_AB0BEYABXX/Data/Intensities/BaseCalls/Aligned/Project_A --od /illumina2/data/111020_SN336_0133_AB0BEYABXX/Data/Intensities/BaseCalls/VariantProjectA --ref /data/pub_data/hg18 -f
@SQ SN:chr1.fa LN:247249719
@SQ SN:chr2.fa LN:242951149
@SQ SN:chr3.fa LN:199501827
@SQ SN:chr4.fa LN:191273063
@SQ SN:chr5.fa LN:180857866
@SQ SN:chr6.fa LN:170899992
@SQ SN:chr7.fa LN:158821424
@SQ SN:chrX.fa LN:154913754
@SQ SN:chr8.fa LN:146274826
@SQ SN:chr9.fa LN:140273252
@SQ SN:chr10.fa LN:135374737
@SQ SN:chr11.fa LN:134452384
@SQ SN:chr12.fa LN:132349534
@SQ SN:chr13.fa LN:114142980
@SQ SN:chr14.fa LN:106368585
@SQ SN:chr15.fa LN:100338915
@SQ SN:chr16.fa LN:88827254
@SQ SN:chr17.fa LN:78774742
@SQ SN:chr18.fa LN:76117153
@SQ SN:chr19.fa LN:63811651
@SQ SN:chr20.fa LN:62435964
@SQ SN:chrY.fa LN:57772954
@SQ SN:chr22.fa LN:49691432
@SQ SN:chr21.fa LN:46944323
@SQ SN:chrM.fa LN:16571
HWI-ST336_133:2:1208:9721:194569 137 chr1.fa 10 25 22M1D17M1D60M * 0 0 CCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA CCFFFFFHHGHHJJJJJJJJJJJDHI?:C8DH8?FEHI>?D@G3?BBCGCB=C@FD7@@?C=?EBDFBCCEAC=?AD;(9?<9<?<938<A8<?##### BC:Z:0 XD:Z:22^A$17^A$60 SM:i:25 AS:i:0
HWI-ST336_133:2:1208:9721:194569 69 chr1.fa 10 0 * =10 0 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGATAGGGATAGGGCTGGGGTGGGGGTTCGGTGTG @@DFFFDHDHHHFHFEHIGIGIIHGIGGGIIG?GGHBF9DACBAFFGGCB6=>CDE########################################### H0:i:255 H1:i:135 H2:i:83 BC:Z:0
HWI-ST336_133:4:2101:19741:191800 153 chr1.fa 12 11 99M *0 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA ################???95(BA;(5(?CA?;6BED?C=HC@(D=IHF=C=EBB289BGF@D9IIHGF?IGGDF?HEECA?JIIIIHGHHHDADDDB? BC:Z:0 XD:Z:99SM:i:11 AS:i:0
I want to use IGV for viewing my BAM file data which I generated by Hiseq2000.
Using ELANDv2, the data was aligned to hg18 and called SNP and small IN/DEL.
However, when I open the BAM file as output data of ELANDv2 on IGV, any data is not shown.
As searching the reason, I could find this suggestion - http://www.broadinstitute.org/softwa...ata/#aliasfile
So, I made the alias file and located the location that page mentioned.
But, the result is same with before.
Is anyone help me?
Below is my sample SAM data.
@HD VN:1.0 SO:coordinate
@PG ID:CASAVA VN:CASAVA-1.8.1 CL:/usr/local/bin/configureBuild.pl --id /illumina2/data/111020_SN336_0133_AB0BEYABXX/Data/Intensities/BaseCalls/Aligned/Project_A --od /illumina2/data/111020_SN336_0133_AB0BEYABXX/Data/Intensities/BaseCalls/VariantProjectA --ref /data/pub_data/hg18 -f
@SQ SN:chr1.fa LN:247249719
@SQ SN:chr2.fa LN:242951149
@SQ SN:chr3.fa LN:199501827
@SQ SN:chr4.fa LN:191273063
@SQ SN:chr5.fa LN:180857866
@SQ SN:chr6.fa LN:170899992
@SQ SN:chr7.fa LN:158821424
@SQ SN:chrX.fa LN:154913754
@SQ SN:chr8.fa LN:146274826
@SQ SN:chr9.fa LN:140273252
@SQ SN:chr10.fa LN:135374737
@SQ SN:chr11.fa LN:134452384
@SQ SN:chr12.fa LN:132349534
@SQ SN:chr13.fa LN:114142980
@SQ SN:chr14.fa LN:106368585
@SQ SN:chr15.fa LN:100338915
@SQ SN:chr16.fa LN:88827254
@SQ SN:chr17.fa LN:78774742
@SQ SN:chr18.fa LN:76117153
@SQ SN:chr19.fa LN:63811651
@SQ SN:chr20.fa LN:62435964
@SQ SN:chrY.fa LN:57772954
@SQ SN:chr22.fa LN:49691432
@SQ SN:chr21.fa LN:46944323
@SQ SN:chrM.fa LN:16571
HWI-ST336_133:2:1208:9721:194569 137 chr1.fa 10 25 22M1D17M1D60M * 0 0 CCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA CCFFFFFHHGHHJJJJJJJJJJJDHI?:C8DH8?FEHI>?D@G3?BBCGCB=C@FD7@@?C=?EBDFBCCEAC=?AD;(9?<9<?<938<A8<?##### BC:Z:0 XD:Z:22^A$17^A$60 SM:i:25 AS:i:0
HWI-ST336_133:2:1208:9721:194569 69 chr1.fa 10 0 * =10 0 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGATAGGGATAGGGCTGGGGTGGGGGTTCGGTGTG @@DFFFDHDHHHFHFEHIGIGIIHGIGGGIIG?GGHBF9DACBAFFGGCB6=>CDE########################################### H0:i:255 H1:i:135 H2:i:83 BC:Z:0
HWI-ST336_133:4:2101:19741:191800 153 chr1.fa 12 11 99M *0 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAA ################???95(BA;(5(?CA?;6BED?C=HC@(D=IHF=C=EBB289BGF@D9IIHGF?IGGDF?HEECA?JIIIIHGHHHDADDDB? BC:Z:0 XD:Z:99SM:i:11 AS:i:0
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