From 5fd40868cfc6f5715ef67e7927d8f43a2a221bdc Mon Sep 17 00:00:00 2001
From: Kedi Cao <kedi.cao@klinik.uni-regensburg.de>
Date: Thu, 20 Feb 2025 12:18:40 +0100
Subject: [PATCH] Update README.md
---
README.md | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 5af8322..9d4839f 100644
--- a/README.md
+++ b/README.md
@@ -138,21 +138,23 @@ As in the snakemake workflow, user can set the k-mer size for customized Algorit
```
popins4snake merge-bams [OPTIONS] input1.bam input2.bam
```
-As part of the contigmap function, `merge-bams` merges the mapped and sorted files from BWA and SAMtools in the contigmap module. This process anchors both ends of each read pair, ensuring that pairs with one end aligned to the reference genome and the other end aligned to the supercontigs are brought together.
+As part of the contigmap function in PopIns and PopIns2, now used in contigmap module in the workflow, `merge-bams` merges the mapped and sorted files from `BWA` and `SAMtools` in the contigmap module. This process anchors both ends of each read pair, ensuring that pairs with one end aligned to the reference genome and the other end aligned to the supercontigs are brought together.
-### The `find-locations` function
+### Functions for `position` module
+The functions below, including `find-locations`,`merge-locations` and `place` functions, are part of the position module in the workflow. Since the workflow now supports optional contamination removal, some intermediate files have changed based on the config conditions. Therefor these functions were adjusted to take files with removed contaminations and aligned to alternative references during the cleaning steps.
+#### The `find-locations` function
```
popins4snake find-locations [OPTIONS] SAMPLE_ID
```
+This funciton anchors the aligned read pairs to the reference and determines the position of the read pairs on the genome from each sample.
-
-### The `merge-locations` function
+#### The `merge-locations` function
```
popins4snake merge-locations [OPTIONS]
```
+This function combines the detected locations of read pairs from all input samples in one file.
-
-### The `place` function
+#### The `place` functions
```
popins4snake place-refalign [OPTIONS]
popins4snake place-splitalign [OPTIONS] SAMPLE_ID
@@ -165,6 +167,7 @@ In brief, the place commands attempt to anker the supercontigs to the samples. A
popins4snake genotype [OPTIONS] SAMPLE_ID
```
The genotype command generates alleles (ALT) of the supercontigs with some flanking reference genome sequence. Then, the reads of a sample are aligned to ALT and the reference genome around the breakpoint (REF). The ratio of alignments to ALT and REF determines a genotype quality and a final genotype prediction per variant per sample.
+Combined with bcftools sort and merge functions, these steps completed the genotype module of the workflow.
--
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