gatk UnifiedGenotyper

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.

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's
this.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

1. Compress your .vcf file using the bgzip program:  

bgzip my.vcf

1.  For more information about the bgzip command, run it with no arguments to  display the usage message.
2. 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 MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determinedit type tag :NAME listing the correct type from among the supported types:

##### 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。