chapmanb
commented
9 years ago Piet;
Thanks for trying out bcbio.variation and for the very complete report. It looks like something is unexpected with your bed file ref.bed. Specifically, do the start/end coordinates in the file contain quotes around them? It looks like we're complaining about "14596 being present as either the start or end of one of the lines. If you clean that up, hopefully it'll continue without any issues and get you the comparison info. Hope this helps.
zeneofa
Hi,
I am trying to compare a set of vcf files to a set of confirmed snps from a genome in a bottle database. I do not have access to the raw fastq file, so I am unsure regarding the filters applied to mapping. I merely have a set of bam files, vcf files a bed region file. I therefore also don't know what post mapping alteration have been performed.
I have have tried to run:
java -jar ~/Downloads/bcbio.variation-0.2.1-standalone.jar variant-compare ref-grading.yaml
where my ref-grading.yaml file contains the following:
dir: out: grading prep: grading/prep experiments:
I get the following error, (I am not familiar with java though):
2015-01-12 16:48:18,299 [INFO ] MLog clients using log4j logging. 2015-01-12 16:48:18,760 [INFO ] State :begin :: {:desc "Starting variation analysis"} 2015-01-12 16:48:18,788 [INFO ] State :clean :: {:desc "Cleaning input VCF: reference"} 2015-01-12 16:48:18,789 [INFO ] State :merge :: {:desc "Merging multiple input files: reference"} 2015-01-12 16:48:18,790 [INFO ] State :prep :: {:desc "Prepare VCF, resorting to genome build: reference"} "ava.lang.NumberFormatException: For input string: "14596 at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:492) at java.lang.Integer.parseInt(Integer.java:527) at bcbio.align.ref$prep_bedline_sort$fn1333.invoke(ref.clj:85) at bcbio.align.ref$sort_bed_file$fn1338$fn1339$fn1344.invoke(ref.clj:98) at clojure.core$sort_by$fn4299.invoke(core.clj:2769) at clojure.lang.AFunction.compare(AFunction.java:49) at java.util.TimSort.countRunAndMakeAscending(TimSort.java:324) at java.util.TimSort.sort(TimSort.java:203) at java.util.TimSort.sort(TimSort.java:173) at java.util.Arrays.sort(Arrays.java:659) at clojure.core$sort.invoke(core.clj:2754) at clojure.core$sort_by.invoke(core.clj:2769) at clojure.core$sort_by.invoke(core.clj:2767) at bcbio.align.ref$sort_bed_file$fn1338$fn1339.invoke(ref.clj:99) at bcbio.align.ref$sort_bed_file$fn1338.invoke(ref.clj:97) at bcbio.align.ref$sort_bed_file.invoke(ref.clj:96) at bcbio.run.broad$gatk_cl_intersect_intervals$fn1816.invoke(broad.clj:56) at clojure.core$map$fn4207.invoke(core.clj:2487) at clojure.lang.LazySeq.sval(LazySeq.java:42) at clojure.lang.LazySeq.seq(LazySeq.java:60) at clojure.lang.RT.seq(RT.java:484) at clojure.core$seq.invoke(core.clj:133) at clojure.core$map$fn4207.invoke(core.clj:2479) at clojure.lang.LazySeq.sval(LazySeq.java:42) at clojure.lang.LazySeq.seq(LazySeq.java:60) at clojure.lang.RT.seq(RT.java:484) at clojure.core$seq.invoke(core.clj:133) at clojure.core$tree_seq$walk4647$fn4648.invoke(core.clj:4475) at clojure.lang.LazySeq.sval(LazySeq.java:42) at clojure.lang.LazySeq.seq(LazySeq.java:60) at clojure.lang.LazySeq.more(LazySeq.java:96) at clojure.lang.RT.more(RT.java:607) at clojure.core$rest.invoke(core.clj:73) at clojure.core$flatten.invoke(core.clj:6478) at bcbio.run.broad$gatk_cl_intersect_intervals.doInvoke(broad.clj:56) at clojure.lang.RestFn.invoke(RestFn.java:425) at bcbio.variation.filter.intervals$select_by_sample.doInvoke(intervals.clj:56) at clojure.lang.RestFn.invoke(RestFn.java:846) at bcbio.variation.combine$dirty_prep_work$run_sample_select1157.invoke(combine.clj:140) at bcbio.variation.combine$dirty_prep_work.invoke(combine.clj:155) at bcbio.variation.combine$gatk_normalize.invoke(combine.clj:187) at bcbio.variation.compare$prepare_vcf_calls$fn7526.invoke(compare.clj:120) at clojure.core$map$fn4207.invoke(core.clj:2487) at clojure.lang.LazySeq.sval(LazySeq.java:42) at clojure.lang.LazySeq.seq(LazySeq.java:60) at clojure.lang.RT.seq(RT.java:484) at clojure.lang.LazilyPersistentVector.create(LazilyPersistentVector.java:31) at clojure.core$vec.invoke(core.clj:354) at bcbio.variation.compare$prepare_vcf_calls.invoke(compare.clj:121) at bcbio.variation.compare$variant_comparison_from_config$iter75827586$fn__7587.invoke(compare.clj:255) at clojure.lang.LazySeq.sval(LazySeq.java:42) at clojure.lang.LazySeq.seq(LazySeq.java:60) at clojure.lang.RT.seq(RT.java:484) at clojure.core$seq.invoke(core.clj:133) at clojure.core$tree_seq$walk4647$fn4648.invoke(core.clj:4475) at clojure.lang.LazySeq.sval(LazySeq.java:42) at clojure.lang.LazySeq.seq(LazySeq.java:60) at clojure.lang.LazySeq.more(LazySeq.java:96) at clojure.lang.RT.more(RT.java:607) at clojure.core$rest.invoke(core.clj:73) at clojure.core$flatten.invoke(core.clj:6478) at bcbio.variation.compare$variant_comparison_from_config.invoke(compare.clj:254) at bcbio.variation.compare$_main.invoke(compare.clj:274) at clojure.lang.AFn.applyToHelper(AFn.java:161) at clojure.lang.AFn.applyTo(AFn.java:151) at clojure.core$apply.invoke(core.clj:617) at bcbio.variation.core$_main.doInvoke(core.clj:35) at clojure.lang.RestFn.applyTo(RestFn.java:137) at bcbio.variation.core.main(Unknown Source)
I have no idea how to start debuggin this, is there some input file format that I am not aware of? Must my reference.fa be truncated to the same chromosomes as indicated in the bed file?
My Aim: To get a good estimate of the false positive/negative rate, as well as possible factors influencing these (such as coverage, entropy of neigbouring regions, mapping quality etc).
Additional information: from the header of the vcf file the reference appears to be hg19 ucsc (which is what I used), it also appears that the additional chromosomes have been removed from the header and the call list in the vcf file (ie only chr1 - 22 + x +y). The ref.vcf and bed was downloaded and appear to have the same ucsc naming convension. My reference is indexed and there exists a gatk dictionary file. Java version (jdk 1.7.0_45). CentosOS, cluster with lustre file system.
Kind Regards, Piet Jones