<![CDATA[SV 结构编译分析]]>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.bam

cram 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
]]>http://an.forum.genostack.com/topic/756/sv-结构编译分析RSS for NodeSat, 13 Jun 2026 09:37:47 GMTFri, 19 Aug 2022 12:18:24 GMT60<![CDATA[Reply to SV 结构编译分析 on Sat, 25 Feb 2023 03:33:06 GMT]]>https://expert.cheekyscientist.com/structural-variant-calling-from-ngs-data/
048cbf12-5b91-4e75-b9c7-9f844419a80a-image.png
split-read

]]>http://an.forum.genostack.com/post/1968http://an.forum.genostack.com/post/1968Sat, 25 Feb 2023 03:33:06 GMT<![CDATA[Reply to SV 结构编译分析 on Sat, 25 Feb 2023 03:07:45 GMT]]>http://www.cs.bilkent.edu.tr/~calkan/teaching/cs681/slides/cs681-Week6.2.pdf
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]]>http://an.forum.genostack.com/post/1966http://an.forum.genostack.com/post/1966Sat, 25 Feb 2023 03:07:45 GMT<![CDATA[Reply to SV 结构编译分析 on Fri, 24 Feb 2023 06:42:16 GMT]]>2453e140-4de5-4b47-974e-ea2fb2e62ea0-image.png
A robust benchmark for detection of germline
large deletions and insertions
https://sci-hub.st/10.1038/s41587-020-0538-8

]]>http://an.forum.genostack.com/post/1960http://an.forum.genostack.com/post/1960Fri, 24 Feb 2023 06:42:16 GMT<![CDATA[Reply to SV 结构编译分析 on Fri, 24 Feb 2023 03:47:43 GMT]]>f4ce4c4c-db74-435d-8df8-c4307d54068e-image.png
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A structural variation reference for medical and population genetics
https://www.nature.com/articles/s41586-020-2287-8

]]>http://an.forum.genostack.com/post/1959http://an.forum.genostack.com/post/1959Fri, 24 Feb 2023 03:47:43 GMT<![CDATA[Reply to SV 结构编译分析 on Fri, 24 Feb 2023 02:38:43 GMT]]>https://gatk.broadinstitute.org/hc/en-us/articles/9022476791323-Structural-Variants
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]]>http://an.forum.genostack.com/post/1958http://an.forum.genostack.com/post/1958Fri, 24 Feb 2023 02:38:43 GMT<![CDATA[Reply to SV 结构编译分析 on Thu, 23 Feb 2023 09:43:01 GMT]]>https://bioinformaticsdotca.github.io/HTG_2021/CBW_HTseq_module5/index.html

]]>http://an.forum.genostack.com/post/1957http://an.forum.genostack.com/post/1957Thu, 23 Feb 2023 09:43:01 GMT<![CDATA[Reply to SV 结构编译分析 on Thu, 23 Feb 2023 09:41:56 GMT]]>https://bioinformaticsdotca.github.io/HTG_2021/CBW_HTseq_module5/index.html

]]>http://an.forum.genostack.com/post/1956http://an.forum.genostack.com/post/1956Thu, 23 Feb 2023 09:41:56 GMT<![CDATA[Reply to SV 结构编译分析 on Thu, 23 Feb 2023 08:51:31 GMT]]>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

]]>http://an.forum.genostack.com/post/1955http://an.forum.genostack.com/post/1955Thu, 23 Feb 2023 08:51:31 GMT<![CDATA[Reply to SV 结构编译分析 on Thu, 23 Feb 2023 06:54:13 GMT]]>[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

]]>http://an.forum.genostack.com/post/1953http://an.forum.genostack.com/post/1953Thu, 23 Feb 2023 06:54:13 GMT