Closed Fred-07 closed 5 years ago
Which versions of R and VariantAnnotation are you using?
On Thu, Jul 18, 2019 at 9:29 PM Fred-07 notifications@github.com wrote:
Hello. I started from a .bam file using the script gridss_separate.sh to perform GRIDSS analysis. I wanted to annotate the SV type in the .vcf file using the commands proposed by D. Cameron.
vcf.file <- "C:/Scratch/NA_12878_duplicates_removed.sv.vcf" vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") gr <- breakpointRanges(vcf)
Warning message: In .breakpointRanges(x, ...) Removing 13731 unpaired breakend variants gridss0bf_5o, gridss0ff_14o, gridss0bb_15o, gridss0bb_17o, gridss0fb_141o, gridss0bb_20o, gridss0ff_23o, gridss0bb_27o, gridss0fb_397o, gridss0bf_145h, gridss0ff_228o, gridss0bf_248o, gridss0bf_314o, gridss0fb_1097o, gridss0bf_382o, gridss0bb_334o, gridss0bf_504o, gridss0ff_497o, gridss0fb_1763o, gridss0ff_608o, gridss0bb_785o, gridss0bf_937o, gridss0bb_797o, gridss0fb_2629o, gridss0bb_820o, gridss0fb_2665o, gridss0bb_842o, gridss0bf_1021o, gridss0bf_1094o, gridss0bb_986o, gridss0bb_1070o, gridss0fb_3431o, gridss0bb_1105o, gridss0bf_1398o, gridss0bf_1422o, gridss0bb_1294o, gridss0fb_4020o, gridss0fb_4068o, gridss0bb_1344o, gridss0bf_1634o, gridss0bf_1638o, gridss0fb_4154o, gridss0fb_4157o, gridss0bf_1641o, gridss0fb_4159o, gridss0fb_4160o, gridss0bf_1643o, gridss0fb_4162o, gridss0bf_1644o, gridss0fb_4167o, gridss0bf_1645o, gridss0fb_4175o, gridss0bf_1648o, gridss0bf_1650o, gridss0fb_4177o, gridss0fb_4178o, gridss0bf_1652o, gridss0fb_4180o, grid [... truncated]
svtype <- simpleEventType(gr) info(vcf)$SIMPLE_TYPE <- NAcharacter
Warning message: info fields with no header: SIMPLE_TYPE
info(vcf[gr$vcfId])$SIMPLE_TYPE <- svtype
Error in [[<-(tmp, name, value = c("DUP", "INS", "INS", "INS", "INS", : 185200 elements in value to replace 0 elements
info(vcf)$SIMPLE_TYPE <- svtype
Error in [[<-(tmp, name, value = c("DUP", "INS", "INS", "INS", "INS", : 185200 elements in value to replace 425839 elements
It is unclear where the gr$vcfId comes from. Does it appear when multiple .bam files are treated in the same analysis? However, after removing the reference to gr$vcfId, there is is another problem.
I tried with the demo data as described below. The problem with gr$vcfId is found with the demo data too.
vcf.file2 <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf2 <- VariantAnnotation::readVcf(vcf.file2, "hg19")
gr2 <- breakpointRanges(vcf2)
Warning message: In .breakpointRanges(x, ...) : Removing 4 unpaired breakend variants gridss8o, gridss14o, gridss27o, gridss31o
svtype2 <- simpleEventType(gr2) info(vcf2)$SIMPLE_TYPE <- NAcharacter
Warning message:
info fields with no header: SIMPLE_TYPE
info(vcf2[gr2$vcfId])$SIMPLE_TYPE <- svtype2
Error in [[<-(tmp, name, value = c("CTX", "DUP", "DUP", "CTX")) :
4 elements in value to replace 0 elements
info(vcf2)$SIMPLE_TYPE <- svtype2
Warning message: info fields with no header: SIMPLE_TYPE
Could you please help to annotate correctly the output of GRIDSS to get a .vcf with SVLEN and SVTYPE
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PapenfussLab/StructuralVariantAnnotation/issues/19?email_source=notifications&email_token=ABOBYOHBXR62TYE64MNYXWDQABHZFA5CNFSM4IEZXHDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G77J6HQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ABOBYOHDPGKKQJZKF2CSPPTQABHZFANCNFSM4IEZXHDA .
R version 3.6.1 (2019-07-05) VariantAnnotation 1.30.1 StructuralVariantAnnotation 1.0.0
callr and processx packages don't compile anymore. The versions are 3.3.0 and 3.4.0 respectively.
Looks like VariantAnnotation 1.30.1 no longer supports writing VCF fields without also writing a matching header. I'll update the script in the next few days.
On Fri, Jul 19, 2019 at 6:06 PM Fred-07 notifications@github.com wrote:
R version 3.6.1 (2019-07-05) VariantAnnotation 1.30.1 StructuralVariantAnnotation 1.0.0
callr and processx packages don't compile anymore. The versions are 3.3.0 and 3.4.0 respectively.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/PapenfussLab/StructuralVariantAnnotation/issues/19?email_source=notifications&email_token=ABOBYOBZFAAMUGFAKIVQLCTQAFYZBA5CNFSM4IEZXHDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2K5H5Q#issuecomment-513135606, or mute the thread https://github.com/notifications/unsubscribe-auth/ABOBYOGLIJFKTHQOR4XS7GLQAFYZBANCNFSM4IEZXHDA .
Thank you Daniel!
Updating https://github.com/PapenfussLab/gridss/commits/master/example/simple-event-annotation.R is working. Sorry for not posting a follow-up on this issue after fixing it.
Hello. I started from a .bam file using the script gridss_separate.sh to perform GRIDSS analysis. I wanted to annotate the SV type in the .vcf file using the commands proposed by D. Cameron.
vcf.file <- "C:/Scratch/NA_12878_duplicates_removed.sv.vcf" vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") gr <- breakpointRanges(vcf)
Warning message: In .breakpointRanges(x, ...) Removing 13731 unpaired breakend variants gridss0bf_5o, gridss0ff_14o, gridss0bb_15o, gridss0bb_17o, gridss0fb_141o, gridss0bb_20o, gridss0ff_23o, gridss0bb_27o, gridss0fb_397o, gridss0bf_145h, gridss0ff_228o, gridss0bf_248o, gridss0bf_314o, gridss0fb_1097o, gridss0bf_382o, gridss0bb_334o, gridss0bf_504o, gridss0ff_497o, gridss0fb_1763o, gridss0ff_608o, gridss0bb_785o, gridss0bf_937o, gridss0bb_797o, gridss0fb_2629o, gridss0bb_820o, gridss0fb_2665o, gridss0bb_842o, gridss0bf_1021o, gridss0bf_1094o, gridss0bb_986o, gridss0bb_1070o, gridss0fb_3431o, gridss0bb_1105o, gridss0bf_1398o, gridss0bf_1422o, gridss0bb_1294o, gridss0fb_4020o, gridss0fb_4068o, gridss0bb_1344o, gridss0bf_1634o, gridss0bf_1638o, gridss0fb_4154o, gridss0fb_4157o, gridss0bf_1641o, gridss0fb_4159o, gridss0fb_4160o, gridss0bf_1643o, gridss0fb_4162o, gridss0bf_1644o, gridss0fb_4167o, gridss0bf_1645o, gridss0fb_4175o, gridss0bf_1648o, gridss0bf_1650o, gridss0fb_4177o, gridss0fb_4178o, gridss0bf_1652o, gridss0fb_4180o, grid [... truncated]
svtype <- simpleEventType(gr) info(vcf)$SIMPLE_TYPE <- NA_character_
Warning message: info fields with no header: SIMPLE_TYPE
info(vcf[gr$vcfId])$SIMPLE_TYPE <- svtype
Error in
[[<-
(*tmp*
, name, value = c("DUP", "INS", "INS", "INS", "INS", : 185200 elements in value to replace 0 elementsinfo(vcf)$SIMPLE_TYPE <- svtype
Error in
[[<-
(*tmp*
, name, value = c("DUP", "INS", "INS", "INS", "INS", : 185200 elements in value to replace 425839 elementsIt is unclear where the gr$vcfId comes from. Does it appear when multiple .bam files are treated in the same analysis? However, after removing the reference to gr$vcfId, there is is another problem.
I tried with the demo data as described below. The problem with gr$vcfId is found with the demo data too.
vcf.file2 <- system.file("extdata", "gridss.vcf", package = "StructuralVariantAnnotation")
vcf2 <- VariantAnnotation::readVcf(vcf.file2, "hg19")
gr2 <- breakpointRanges(vcf2)
Warning message: In .breakpointRanges(x, ...) : Removing 4 unpaired breakend variants gridss8o, gridss14o, gridss27o, gridss31o
svtype2 <- simpleEventType(gr2) info(vcf2)$SIMPLE_TYPE <- NA_character_
Warning message:
info fields with no header: SIMPLE_TYPE
info(vcf2[gr2$vcfId])$SIMPLE_TYPE <- svtype2
Error in
[[<-
(*tmp*
, name, value = c("CTX", "DUP", "DUP", "CTX")) :4 elements in value to replace 0 elements
info(vcf2)$SIMPLE_TYPE <- svtype2
Warning message: info fields with no header: SIMPLE_TYPE
Could you please help to annotate correctly the output of GRIDSS to get a .vcf with SVLEN and SVTYPE