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AnnotationStatistics/README.md

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@@ -18,6 +18,25 @@ find ../annotationAnaysisSNP_rst/* | grep json > all_json_file_list_SNP.txt
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./annotationAnaysisSNP SV_excel all_combine.json title_str > final_excel_SV.tsv
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```
2020

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## Statistics on the number of variants in fixed-length window intervals
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(1) Using 500/1000/10000/100000 as window lengths, count the number of variants in each window on each chromosome, and the number of variants distributed in each frequency class
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```
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regulation_region/submit_find_out.py
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```
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(2) Combine all the analysis results in all windows
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```
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regulation_region/cmb_region_variants.py
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```
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(3) Split the results according to the frequency level
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```
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regulation_region/split_region_variants_col.py
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```
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(4) Sort the number of variants distributed in frequency classes and fetch the top 1000 windows with the most variants
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```
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regulation_region/submit_fetch_1000.py
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```
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## For SVs:
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(1)Execute annotation statistics, where "SV_var.vcf" is the joint SV file, "annoteSV_sesult.tsv" is the annotation result generate by annoteSV, and "output_fn.json" is the statistics result.
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```

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