GATK

一、简介

Genome Analysis Toolkit
官网:
https://software.broadinstitute.org/gatk/guide/topic?name=tutorials

GATK使用方法详解(原始数据的处理)
http://www.plob.org/article/7009.html

二、Calling

两个工具:
UnifiedGenotyper
Can’t get calls for multiple records at same position in the alleles input file; UnifiedGenotyper
One way is to separate out the SNPs and indels then re-merge them.
这是UG的硬伤呀,如果生成vcf中有两个点位置一样,则只能call其中一个,插入或删除突变的位置跟点突变的位置一样,则只能call 点突变,所以他们才建议插入删除突变单独跑
http://gatkforums.broadinstitute.org/gatk/discussion/2305/cant-get-calls-for-multiple-records-at-same-position-in-the-alleles-input-file-unifiedgenotyper

和HaplotypeCaller
3.HaplotypeCaller说明

https://software.broadinstitute.org/gatk/gatkdocs/3.7-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php

java -jar -Xmx8g /bioinfo/software/bin/GenomeAnalysisTK.jar
-l INFO
-T HaplotypeCaller
-R /bioinfo/data/iGenomes/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa -I NA14637-5_sort_realign_clipped.bam
-pairHMM VECTOR_LOGLESS_CACHING
-stand_emit_conf 10
-stand_call_conf 30.0
-D /bioinfo/data/SNP/SNP146_GRCh37.vcf
-L /home/qqin/genopipe_py/genopipe/data/brca_LP.target.zerobased.bed
-o /home/qqin/data_analysis/20161205_braca_lp_evaluation/1.analysis/9.call_variant/NA14637-5.g.vcf
-bamout /home/qqin/data_analysis/20161205_braca_lp_evaluation/1.analysis/9.call_variant/NA14637-5_sort_realign_recalibrate_clipped_hc.bam
–max_alternate_alleles 10
-A StrandBiasBySample
-gt_mode DISCOVERY
-S LENIENT

stand_emit_conf 位点得分低于这个值就不显示到vcf里面去

为什么UnifiedGenotyper算出来的DP值要比HaplotypeCaller的小?

HaplotypeCaller根据bam文件有个重新比对的过程,
max_alternate_alleles 默认的为6

三、其他
。。。

四、讨论

1.depth大于AD
http://gatkforums.broadinstitute.org/gatk/discussion/1235/i-expect-to-see-a-variant-at-a-specific-site-but-its-not-getting-called
https://software.broadinstitute.org/gatk/guide/article?id=5484

2.如何让gatk更快
http://gatkforums.broadinstitute.org/gatk/discussion/1975/how-can-i-use-parallelism-to-make-gatk-tools-run-faster
实际上有3个参数加速的参数:
-nt / –num_threads
-nct / –num_cpu_threads_per_data_thread

五、报错:
1.Input files reads and reference have incompatible contigs

原因:

解决办法:

 

参考资料:

http://gatkforums.broadinstitute.org/gatk/discussion/6546/input-files-reads-and-reference-have-incompatible-contigs

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