d-cameron
commented
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)$SIMPLE_TYPE <- svtype2
Warning message: info fields with no header: SIMPLE_TYPE
Could you please help to annotate correctly the output of GRIDSS to get a .vcf with SVLEN and SVTYPE
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Fred-07
Hello. I started from a .bam file using the script gridss_separate.sh to perform GRIDSS analysis. I wanted to annotate the SV type in the .vcf file using the commands proposed by D. Cameron.
vcf.file <- "C:/Scratch/NA_12878_duplicates_removed.sv.vcf" vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") gr <- breakpointRanges(vcf)Warning message: In .breakpointRanges(x, ...) Removing 13731 unpaired breakend variants gridss0bf_5o, gridss0ff_14o, gridss0bb_15o, gridss0bb_17o, gridss0fb_141o, gridss0bb_20o, gridss0ff_23o, gridss0bb_27o, gridss0fb_397o, gridss0bf_145h, gridss0ff_228o, gridss0bf_248o, gridss0bf_314o, gridss0fb_1097o, gridss0bf_382o, gridss0bb_334o, gridss0bf_504o, gridss0ff_497o, gridss0fb_1763o, gridss0ff_608o, gridss0bb_785o, gridss0bf_937o, gridss0bb_797o, gridss0fb_2629o, gridss0bb_820o, gridss0fb_2665o, gridss0bb_842o, gridss0bf_1021o, gridss0bf_1094o, gridss0bb_986o, gridss0bb_1070o, gridss0fb_3431o, gridss0bb_1105o, gridss0bf_1398o, gridss0bf_1422o, gridss0bb_1294o, gridss0fb_4020o, gridss0fb_4068o, gridss0bb_1344o, gridss0bf_1634o, gridss0bf_1638o, gridss0fb_4154o, gridss0fb_4157o, gridss0bf_1641o, gridss0fb_4159o, gridss0fb_4160o, gridss0bf_1643o, gridss0fb_4162o, gridss0bf_1644o, gridss0fb_4167o, gridss0bf_1645o, gridss0fb_4175o, gridss0bf_1648o, gridss0bf_1650o, gridss0fb_4177o, gridss0fb_4178o, gridss0bf_1652o, gridss0fb_4180o, grid [... truncated]
svtype <- simpleEventType(gr) info(vcf)$SIMPLE_TYPE <- NA_character_Warning message: info fields with no header: SIMPLE_TYPE
info(vcf[gr$vcfId])$SIMPLE_TYPE <- svtypeError in
[[<-(*tmp*, name, value = c("DUP", "INS", "INS", "INS", "INS", : 185200 elements in value to replace 0 elementsinfo(vcf)$SIMPLE_TYPE <- svtypeError in
[[<-(*tmp*, name, value = c("DUP", "INS", "INS", "INS", "INS", : 185200 elements in value to replace 425839 elementsIt is unclear where the gr$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])$SIMPLE_TYPE <- svtype2Error in
[[<-(*tmp*, name, value = c("CTX", "DUP", "DUP", "CTX")) :4 elements in value to replace 0 elements
info(vcf2)$SIMPLE_TYPE <- svtype2Warning 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