SV 结构编译分析
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sv-pipeline需要cram 先生产cram
bwa mem -R '@RG\tID:foo\tSM:bar\tLB:library1' human_g1k_v37_20_42220611-42542245.fasta NA12878.20slice.30X.fastq > NA12878.sam samtools sort NA12878.sam -o NA12878.bam samtools view -T human_g1k_v37_20_42220611-42542245.fasta -C -o NA12878.cram NA12878.bamcram 需要参考基因组的cache 用samtools的工具处理
~/Downloads/src/samtools/samtools/misc/seq_cache_populate.pl human_g1k_v37_20_42220611-42542245.fasta -root cache/ tar cvzf cache.tar.gz cache -
[smoove] 2023/02/23 03:49:12 Error: failed to build insert size histogram for paired-end reads.
Please ensure BAM file (NA12878.cram) has inward facing, paired-end reads.
需要双端序列 -
SV is generally defined as 50 bp or longer genomic variation and is categorized into 5 types: insertions, deletions, duplications, inversions, and translocations
https://academic.oup.com/gigascience/article/8/9/giz110/5565134?login=false
Evaluation of computational genotyping of structural variation for clinical diagnoses
使用短读长 发下新的SV还处于早期
Methods for the de novo detection of SVs are still in their infancy -
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A structural variation reference for medical and population genetics
https://www.nature.com/articles/s41586-020-2287-8 -
A robust benchmark for detection of germline
large deletions and insertions
https://sci-hub.st/10.1038/s41587-020-0538-8 -
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