fixed notes in yleaf

docs/search.json

@@ -256,7 +256,7 @@
     "href": "yleaf.html#what-is-yleaf",
     "title": "10  Y-chromosomal haplogroup inference with Yleaf",
     "section": "10.3 What is Yleaf?",
-    "text": "10.3 What is Yleaf?\nYleaf is a python-based tool for Linux for high-resolution NRY SNP calling and haplogroup inference from NGS data, independent of library and sequencing methods\n\n10.3.1 What are the advantage of using Yleaf?\n\npublicly available\nautomated\nuser-friendly\ncustomisable\nversatile\nmultithreading option\nbuilt-in batch option\noptimized for large NGS data sets such as whole genomes\n\n\n\n10.3.2 How does Yleaf compare to other tools?\nYleaf was tested on modern and ancient published datasets, and produced high concordance in NRY-SNP calling compared to well-established tools such as SAMtools/BCFtools (Li et al. 2009), and GATK HaplotypeCaller (McKenna et al. 2010). Yleaf called the lowest number of markers due to stringent options set, however it also appears to provide the highest overall accuracy\n\n\n10.3.3 How does Yleaf work?\n\n\n\n\n\n\nNote\n\n\n\n\nYleaf requires python 3.6 and currently only works on Linux\nYleaf works with both raw and aligned sequencing data in a single command\nIt accepts raw fastq files, bam, cram and vcf files\nThe batch function allows you to provide a path to a folder and it will pick up all the files sharing the same extension\nThe raw reads are aligned against the reference human genome (either hg19 or hg38) with minimap2 using default settings, which creates a SAM file. (There is also a multi-threading option -t)\nThe SAM file is converted to a BAM file with SAMtools, sorted and indexed.\n\n\n\n\n\n\n\n\n\nNote\n\n\n\n\nFor ancient DNA it is advised to rather supply Yleaf with your quality-filtered BAM files\nThe BAM file is filtered on reads only aligning to the Y-chromosome.\nSAMtools mpileup function creates a raw data file for variant calling.\nYleaf has a function embedded to perform variant calling using the generated pileup file\nAn output folder is created containing output files in the root path for each of the input files."
+    "text": "10.3 What is Yleaf?\nYleaf is a python-based tool for Linux for high-resolution NRY SNP calling and haplogroup inference from NGS data, independent of library and sequencing methods\n\n10.3.1 What are the advantage of using Yleaf?\n\npublicly available\nautomated\nuser-friendly\ncustomisable\nversatile\nmultithreading option\nbuilt-in batch option\noptimized for large NGS data sets such as whole genomes\n\n\n\n10.3.2 How does Yleaf compare to other tools?\nYleaf was tested on modern and ancient published datasets, and produced high concordance in NRY-SNP calling compared to well-established tools such as SAMtools/BCFtools (Li et al. 2009), and GATK HaplotypeCaller (McKenna et al. 2010). Yleaf called the lowest number of markers due to stringent options set, however it also appears to provide the highest overall accuracy\n\n\n10.3.3 How does Yleaf work?\n\n\n\n\n\n\nNote\n\n\n\nYleaf requires python 3.6 and currently only works on Linux\n\n\n\nYleaf works with both raw and aligned sequencing data in a single command\nIt accepts raw fastq files, bam, cram and vcf files\nThe batch function allows you to provide a path to a folder and it will pick up all the files sharing the same extension\nThe raw reads are aligned against the reference human genome (either hg19 or hg38) with minimap2 using default settings, which creates a SAM file. (There is also a multi-threading option -t)\nThe SAM file is converted to a BAM file with SAMtools, sorted and indexed.\n\n\n\n\n\n\n\nNote\n\n\n\nFor ancient DNA it is advised to rather supply Yleaf with your quality-filtered BAM files\n\n\n\nThe BAM file is filtered on reads only aligning to the Y-chromosome.\nSAMtools mpileup function creates a raw data file for variant calling.\nYleaf has a function embedded to perform variant calling using the generated pileup file\nAn output folder is created containing output files in the root path for each of the input files."
   },
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     "objectID": "yleaf.html#installation-and-first-use",

docs/yleaf.html

@@ -355,16 +355,16 @@ <h3 data-number="10.3.3" class="anchored" data-anchor-id="how-does-yleaf-work"><
 </div>
 </div>
 <div class="callout-body-container callout-body">
+<p>Yleaf requires python 3.6 and currently only works on Linux</p>
+</div>
+</div>
 <ul>
-<li>Yleaf requires python 3.6 and currently only works on Linux</li>
 <li>Yleaf works with both raw and aligned sequencing data in a single command</li>
 <li>It accepts raw fastq files, bam, cram and vcf files</li>
 <li>The batch function allows you to provide a path to a folder and it will pick up all the files sharing the same extension</li>
 <li>The raw reads are aligned against the reference human genome (either hg19 or hg38) with minimap2 using default settings, which creates a SAM file. (There is also a multi-threading option -t)</li>
 <li>The SAM file is converted to a BAM file with SAMtools, sorted and indexed.</li>
 </ul>
-</div>
-</div>
 <div class="callout callout-style-default callout-note callout-titled">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -375,15 +375,15 @@ <h3 data-number="10.3.3" class="anchored" data-anchor-id="how-does-yleaf-work"><
 </div>
 </div>
 <div class="callout-body-container callout-body">
+<p>For ancient DNA it is advised to rather supply Yleaf with your quality-filtered BAM files</p>
+</div>
+</div>
 <ul>
-<li>For ancient DNA it is advised to rather supply Yleaf with your quality-filtered BAM files</li>
 <li>The BAM file is filtered on reads only aligning to the Y-chromosome.</li>
 <li>SAMtools mpileup function creates a raw data file for variant calling.</li>
 <li>Yleaf has a function embedded to perform variant calling using the generated pileup file</li>
 <li>An output folder is created containing output files in the root path for each of the input files.</li>
 </ul>
-</div>
-</div>
 </section>
 </section>
 <section id="installation-and-first-use" class="level2" data-number="10.4">

yleaf.qmd

@@ -44,21 +44,25 @@ Yleaf was tested on modern and ancient published datasets, and produced high con
 ### How does Yleaf work?
 
 :::{.callout-note}
-- Yleaf requires python 3.6 and currently only works on Linux
+Yleaf requires python 3.6 and currently only works on Linux
+:::
+
 -   Yleaf works with both raw and aligned sequencing data in a single command
 -   It accepts raw fastq files, bam, cram and vcf files
 -   The batch function allows you to provide a path to a folder and it will pick up all the files sharing the same extension
 -   The raw reads are aligned against the reference human genome (either hg19 or hg38) with minimap2 using default settings, which creates a SAM file. (There is also a multi-threading option -t)
 -   The SAM file is converted to a BAM file with SAMtools, sorted and indexed.
-::: 
+
 
 :::{.callout-note}
-- For ancient DNA it is advised to rather supply Yleaf with your quality-filtered BAM files
+For ancient DNA it is advised to rather supply Yleaf with your quality-filtered BAM files
+:::
+
 - The BAM file is filtered on reads only aligning to the Y-chromosome.
 - SAMtools mpileup function creates a raw data file for variant calling.
 - Yleaf has a function embedded to perform variant calling using the generated pileup file
 - An output folder is created containing output files in the root path for each of the input files.
-:::
+
 
 ## Installation and first use