使用 UnifiedGenotyper注意如下:
(1) 输入:
.recalibration.bam
(2)输入:
.recalibration.bai
(3)dbSNP: vcf
dbsnp,有头部;有与DNA一样的染色体顺序;有idx文件;
UnifiedGenotyper Unable to read index file, for input source: vcf.idx
Sorry for the delayed response. It turns out that this is a problem with OS-level file locking support in some environments. We ran into this at the Broad, which is why the devs added the check. There is a hidden argument called --disableAutoIndexCreationAndLockingWhenReadingRods that disables index auto-creation and related file locking when reading vcfs. If all index files are pre-existing, and no concurrent processes will ever update any of the indices, it should be safe to use this argument.
Ack, sorry @albertoap, I gave you the variable name instead of the argument name. Please try again using --disable_auto_index_creation_and_locking_when_reading_rods, that should do the trick.
(1) 输入:
.recalibration.bam
(2)输入:
.recalibration.bai
(3)dbSNP: vcf
dbsnp,有头部;有与DNA一样的染色体顺序;有idx文件;
UnifiedGenotyper Unable to read index file, for input source: vcf.idx
Sorry for the delayed response. It turns out that this is a problem with OS-level file locking support in some environments. We ran into this at the Broad, which is why the devs added the check. There is a hidden argument called --disableAutoIndexCreationAndLockingWhenReadingRods that disables index auto-creation and related file locking when reading vcfs. If all index files are pre-existing, and no concurrent processes will ever update any of the indices, it should be safe to use this argument.
Ack, sorry @albertoap, I gave you the variable name instead of the argument name. Please try again using --disable_auto_index_creation_and_locking_when_reading_rods, that should do the trick.
I have a feeling I just need to import something else at the top of the .scala file, but I have no idea what it would be.
EDIT: Nevermind, realized I have to use the shortName, not the variable name when working with CommonArguments. So it'sthis.disable_auto_index_creation_and_locking_when_reading_rods = true
Hi I found IGVTools, best for VCF indexing.
igvtools can be run from the command line or IGV itself (File>Run igvtools...) After launching, choose the Index command and browse to your .vcf file. The index file (.idx) will be created in the same directory as the .vcf file.
java -Xmx50g -jar /share_bio/unisvx4/xiehb_kiz/zhouzhy/software/GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar
-R /share_bio/unisvx4/xiehb_kiz/zhouzhy/reference_genome/pig/Sus_scrofa.Sscrofa10.2.dna.toplevel.fa
--genotype_likelihoods_model BOTH
--num_threads 5 -T UnifiedGenotyper
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKF1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKF2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKF3.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKM1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKM2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKU1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKU2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF3.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF4.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF5.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF6.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF7.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF8.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNM1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNM2.recalibration.bam
-mbq 20
--dbsnp /home/zhouzhy/wd/pighisat2/bwa_align/dbsnp/Sus_scrofa.vcf
-stand_call_conf 10 -stand_emit_conf 10 -L 11
-o F0.gatk_chrCHROM_UnifiedGenotyper.vcf
MESSAGE: Unable to read index file, for input source: /home/zhouzhy/wd/pighisat2/bwa_align/dbsnp/Sus_scrofa.vcf.idx
http://data.broadinstitute.org/igv/projects/downloads/
igv, igvtools 是不同的。
-R /share_bio/unisvx4/xiehb_kiz/zhouzhy/reference_genome/pig/Sus_scrofa.Sscrofa10.2.dna.toplevel.fa
--genotype_likelihoods_model BOTH
--num_threads 5 -T UnifiedGenotyper
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKF1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKF2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKF3.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKM1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKM2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKU1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DKU2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF2.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF3.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF4.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF5.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF6.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF7.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNF8.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNM1.recalibration.bam
-I /home/zhouzhy/wd/pig_imprinting/pig_clean_data/DNM2.recalibration.bam
-mbq 20
--dbsnp /home/zhouzhy/wd/pighisat2/bwa_align/dbsnp/Sus_scrofa.vcf
-stand_call_conf 10 -stand_emit_conf 10 -L 11
-o F0.gatk_chrCHROM_UnifiedGenotyper.vcf
MESSAGE: Unable to read index file, for input source: /home/zhouzhy/wd/pighisat2/bwa_align/dbsnp/Sus_scrofa.vcf.idx
- Compress your .vcf file using the
bgzip
program:
For more information about thebgzip my.vcf
bgzip
command, run it with no arguments to display the usage message. - Create a tabix index file for the bgzip-compressed VCF (.vcf.gz):
tabix -p vcf my.vcf.gz
http://data.broadinstitute.org/igv/projects/downloads/
igv, igvtools 是不同的。
##### ERROR Name FeatureType Documentation
##### ERROR BCF2 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_bcf2_BCF2Codec.html
##### ERROR VCF VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_vcf_VCFCodec.html
##### ERROR VCF3 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_vcf_VCF3Codec.html
##### ERROR ------------------------------------------------------------------------------------------
原因:
dbsnp文件缺少头部:
##fileformat=VCFv4.0
##source=dbSNP
##dbSNP_BUILD_ID=145
##reference=GCF_000003025.5
##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf
##INFO=<ID=RSPOS,Number=1,Type=Integer,Description="Chr position reported in dbSNP">
##INFO=<ID=RV,Number=0,Type=Flag,Description="RS orientation is reversed">
##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property. Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf">
##INFO=<ID=GENEINFO,Number=.,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
##INFO=<ID=dbSNPBuildID,Number=1,Type=Integer,Description="First dbSNP Build for RS">
##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated. This bit is set if the variant has 2+ minor allele count based on frequency or genotype data.">
#CHROM POS ID REF ALT QUAL FILTER INFO
加上头部就可以了了。