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@@ -279,7 +279,7 @@ <h2 id="usage">Usage</h2>
 </code></pre>
 <pre><code>## 
 ## Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
-## Version: 1.18 (using htslib 1.18)
+## Version: 1.19 (using htslib 1.19)
 ## 
 ## Usage:   bcftools [--version|--version-only] [--help] &lt;command&gt; &lt;argument&gt;
 ## 
@@ -332,7 +332,7 @@ <h2 id="getting-help">Getting help</h2>
 its parameters.</p>
 <pre><code class="language-bash">man bcftools | grep &quot;LIST OF COMMANDS&quot; -B 1984
 </code></pre>
-<pre><code>## troff: &lt;standard input&gt;:2322: warning [p 23, 10.5i]: can't break line
+<pre><code>## troff: &lt;standard input&gt;:2327: warning [p 24, 2.2i]: can't break line
 ## BCFTOOLS(1)                                                        BCFTOOLS(1)
 ## 
 ## NAME
@@ -362,8 +362,8 @@ <h2 id="getting-help">Getting help</h2>
 ##        (stdout). Several commands can thus be  combined  with  Unix pipes.
 ## 
 ##    VERSION
-##        This manual page was last updated 2023-07-25 and refers to bcftools git
-##        version 1.18.
+##        This manual page was last updated 2023-12-12 and refers to bcftools git
+##        version 1.19.
 ## 
 ##    BCF1
 ##        The obsolete BCF1 format output by versions of samtools &lt;= 0.1.19 is
@@ -447,25 +447,25 @@ <h2 id="comparing-output-types">Comparing output types</h2>
 <pre><code class="language-bash">time bcftools convert --threads 2 -O b -o eg/1kgp.bcf eg/1kgp.vcf
 </code></pre>
 <pre><code>## 
-## real 0m14.143s
-## user 0m24.448s
-## sys  0m1.758s
+## real 0m12.891s
+## user 0m24.601s
+## sys  0m1.695s
 </code></pre>
 <p>VCF to uncompressed BCF.</p>
 <pre><code class="language-bash">time bcftools convert --threads 2 -O u -o eg/1kgp.un.bcf eg/1kgp.vcf
 </code></pre>
 <pre><code>## 
-## real 0m11.901s
-## user 0m24.119s
-## sys  0m1.667s
+## real 0m10.736s
+## user 0m23.899s
+## sys  0m1.803s
 </code></pre>
 <p>VCF to compressed VCF.</p>
 <pre><code class="language-bash">time bcftools convert --threads 2 -O z -o eg/1kgp.vcf.gz eg/1kgp.vcf
 </code></pre>
 <pre><code>## 
-## real 0m17.734s
-## user 0m31.088s
-## sys  0m2.235s
+## real 0m15.329s
+## user 0m28.735s
+## sys  0m2.260s
 </code></pre>
 <p>File sizes</p>
 <pre><code class="language-bash">du -h eg/1kgp.*
@@ -774,18 +774,18 @@ <h3 id="subset-variants-within-a-specific-genomic-region">Subset variants within
 </code></pre>
 <pre><code>## 31036
 ## 
-## real 0m0.071s
+## real 0m0.057s
 ## user 0m0.063s
-## sys  0m0.020s
+## sys  0m0.004s
 </code></pre>
 <p><code>bcftools view</code> with <code>-t</code> streams the entire file, so is much slower.</p>
 <pre><code class="language-bash">time bcftools view -H -t 1:55000000-56000000 eg/1kgp.bcf | wc -l
 </code></pre>
 <pre><code>## 31036
 ## 
-## real 0m3.073s
-## user 0m3.041s
-## sys  0m0.043s
+## real 0m2.844s
+## user 0m2.811s
+## sys  0m0.044s
 </code></pre>
 <p>Use commas to list more than one loci.</p>
 <pre><code class="language-bash">bcftools view -H -r 1:10000-50000,1:100000-200000,1:55000000-56000000 eg/1kgp.bcf | wc -l
@@ -1198,7 +1198,7 @@ <h2 id="check-whether-the-ref-sequence-is-correct">Check whether the REF sequenc
 <pre><code class="language-bash">bcftools norm -f eg/test_31.fa -c w eg/incorrect.vcf &gt; /dev/null
 </code></pre>
 <pre><code>## REF_MISMATCH 1000000 151 G   T
-## Lines   total/split/realigned/skipped:   10022/0/851/0
+## Lines   total/split/joined/realigned/skipped:    10022/0/0/851/0
 </code></pre>
 <h2 id="sorting">Sorting</h2>
 <p>BCFtools has a <code>sort</code> function but the usage does not indicate the
@@ -1214,23 +1214,23 @@ <h2 id="sorting">Sorting</h2>
 <pre><code>## [W::vcf_parse_info] INFO 'GENE' is not defined in the header, assuming Type=String
 ## [W::vcf_parse_info] INFO 'INHERITANCE' is not defined in the header, assuming Type=String
 ## [W::vcf_parse_info] INFO 'MIM' is not defined in the header, assuming Type=String
-## [W::vcf_parse_format] FORMAT 'DS' at 10:123256215 is not defined in the header, assuming Type=String
-## [W::vcf_parse_format] FORMAT 'GL' at 10:123256215 is not defined in the header, assuming Type=String
+## [W::vcf_parse_format_dict2] FORMAT 'DS' at 10:123256215 is not defined in the header, assuming Type=String
+## [W::vcf_parse_format_dict2] FORMAT 'GL' at 10:123256215 is not defined in the header, assuming Type=String
+## 19   19613381    rs892022    G   A   116.4   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.324;DB;DP=19;Dels=0;FS=0;HRun=0;HaplotypeScore=0.9996;MQ0=0;MQ=60;MQRankSum=-0.787;QD=6.13;ReadPosRankSum=-0.88;set=variant2    GT:AD:DP:GQ:PL  0/1:14,5:19:99:146,0,473
 ## 1    34189957    rs11346874  AG  A   210.16  PASS    AC=2;AF=1;AN=2;DB;DP=7;FS=0;HRun=4;HaplotypeScore=18.582;MQ0=0;MQ=60;QD=30.02;set=variant   GT:AD:DP:GQ:PL  1/1:0,7:7:21.06:252,21,0
-## 14   21967438    rs3168880   G   A   264.93  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-2.493;DB;DP=28;Dels=0;FS=0;HRun=0;HaplotypeScore=0.734;MQ0=0;MQ=60;MQRankSum=0.847;QD=9.46;ReadPosRankSum=-0.659;set=variant2    GT:AD:DP:GQ:PL  0/1:17,11:28:99:295,0,537
-## 2    86360225    rs2241438   A   G   102.42  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.922;DB;DP=8;Dels=0;FS=0;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=0.922;QD=12.8;ReadPosRankSum=-1.638;set=variant2  GT:AD:DP:GQ:PL  0/1:4,4:8:99:132,0,125
-## 9    68429175    rs79456414  A   C   634.54  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=3.421;DB;DP=103;Dels=0;FS=1.106;HRun=0;HaplotypeScore=2.7547;MQ0=1;MQ=56.56;MQRankSum=0.326;QD=6.16;ReadPosRankSum=-0.587;set=variant2    GT:AD:DP:GQ:PL  0/1:77,26:103:99:665,0,2168
-## 4    10027643    rs6449237   A   G   71.03   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.135;DB;DP=12;Dels=0;FS=2.817;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=-0.529;QD=5.92;ReadPosRankSum=0.529;set=variant2 GT:AD:DP:GQ:PL  0/1:7,5:12:99:101,0,215
-## 3    33768909    rs73055665  A   G   72.08   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.322;DB;DP=8;Dels=0;FS=0;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=-1.221;QD=9.01;ReadPosRankSum=-0.322;set=variant2 GT:AD:DP:GQ:PL  0/1:3,5:8:95.09:102,0,95
-## 11   56468155    rs11228732  T   G   528.96  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=3.924;DB;DP=78;Dels=0;FS=0;HRun=1;HaplotypeScore=2.8278;MQ0=4;MQ=51.64;MQRankSum=1.612;QD=6.78;ReadPosRankSum=-0.794;set=variant2 GT:AD:DP:GQ:PL  0/1:54,24:78:99:559,0,1468
-## 2    96679384    rs2579517   C   T   150.1   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-0.322;DB;DP=8;Dels=0;FS=0;HRun=2;HaplotypeScore=1.9468;MQ0=0;MQ=56.28;MQRankSum=1.92;QD=18.76;ReadPosRankSum=0.322;set=variant2  GT:AD:DP:GQ:PL  0/1:3,5:8:91.23:180,0,91
-## 21   47328990    rs9976042   T   G   69.8    PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.727;DB;DP=4;Dels=0;FS=0;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=-0.727;QD=17.45;ReadPosRankSum=0.727;set=variant2 GT:AD:DP:GQ:PL  0/1:1,3:4:27.28:100,0,27
-## 5    34811131    rs35607113  G   A   2344.45 PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.53;DB;DP=201;Dels=0;FS=1.104;HRun=0;HaplotypeScore=1.9958;MQ0=0;MQ=58.79;MQRankSum=-0.101;QD=11.66;ReadPosRankSum=0.935;set=variant2    GT:AD:DP:GQ:PL  0/1:99,102:201:99:2374,0,2402
+## 5    160044855   rs1363199   G   A   426.96  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-2.916;DB;DP=34;Dels=0;FS=1.591;HRun=1;HaplotypeScore=0;MQ0=0;MQ=59.45;MQRankSum=-0.776;QD=12.56;ReadPosRankSum=0.293;set=variant2    GT:AD:DP:GQ:PL  0/1:18,16:34:99:457,0,463
+## 19   2110019 rs2074958   T   C   140.73  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-0.336;DB;DP=10;Dels=0;FS=10.792;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=0.851;QD=14.07;ReadPosRankSum=0.103;set=variant2   GT:AD:DP:GQ:PL  0/1:5,5:10:99:171,0,168
+## 5    176721272   rs11740250  G   C   867.88  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.045;DB;DP=60;Dels=0;FS=1.139;HRun=0;HaplotypeScore=2.8535;MQ0=0;MQ=59.23;MQRankSum=1.204;QD=14.46;ReadPosRankSum=1.293;set=variant2 GT:AD:DP:GQ:PL  0/1:27,33:60:99:898,0,720
+## 3    191075656   rs13434281  G   A   88.64   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-2.383;DB;DP=10;Dels=0;FS=0;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=0.365;QD=8.86;ReadPosRankSum=-0.633;set=variant2    GT:AD:DP:GQ:PL  0/1:6,4:10:99:119,0,217
+## 6    32188099    rs430916    C   T   854.23  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-4.977;DB;DP=85;Dels=0;FS=3.074;HRun=2;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=0.634;QD=10.05;ReadPosRankSum=-0.607;set=variant2   GT:AD:DP:GQ:PL  0/1:48,37:85:99:884,0,1432
+## 5    173258  rs6893369   A   G   154.95  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=0.323;DB;DP=14;Dels=0;FS=0;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=-0.452;QD=11.07;ReadPosRankSum=0.452;set=variant2    GT:AD:DP:GQ:PL  0/1:8,6:14:99:185,0,263
+## 16   8953081 rs8097  C   G   150.07  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=-0.741;DB;DP=10;Dels=0;FS=0;HRun=0;HaplotypeScore=0;MQ0=0;MQ=60;MQRankSum=-0.741;QD=15.01;ReadPosRankSum=-0.365;set=variant2  GT:AD:DP:GQ:PL  0/1:4,6:10:68.47:180,0,68
+## 3    52228150    rs411457    A   T   164.03  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=2.001;DB;DP=14;Dels=0;FS=0;HRun=1;HaplotypeScore=0;MQ0=0;MQ=58.2;MQRankSum=-0.065;QD=11.72;ReadPosRankSum=-0.452;set=variant2 GT:AD:DP:GQ:PL  0/1:8,6:14:99:194,0,206
 </code></pre>
 <p>Sort.</p>
 <pre><code class="language-bash">bcftools sort eg/Pfeiffer_shuf.vcf &gt; eg/Pfeiffer_sorted.vcf
 </code></pre>
-<pre><code>## Writing to /tmp/bcftools.L29NCK
+<pre><code>## Writing to /tmp/bcftools.FlkYqD
 ## Merging 1 temporary files
 ## Cleaning
 ## Done
@@ -1416,9 +1416,9 @@ <h2 id="remove-header-info">Remove header info</h2>
 ## ##INFO=&lt;ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"&gt;
 ## ##contig=&lt;ID=1000000,length=1000000&gt;
 ## ##source=HaplotypeCaller
-## ##bcftools_viewVersion=1.18+htslib-1.18
-## ##bcftools_viewCommand=view -h eg/aln.hc.vcf.gz; Date=Mon Mar 25 07:36:52 2024
-## ##bcftools_viewCommand=view -h -; Date=Mon Mar 25 07:36:52 2024
+## ##bcftools_viewVersion=1.19+htslib-1.19
+## ##bcftools_viewCommand=view -h eg/aln.hc.vcf.gz; Date=Mon Mar 25 23:27:24 2024
+## ##bcftools_viewCommand=view -h -; Date=Mon Mar 25 23:27:24 2024
 ## #CHROM   POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  test
 </code></pre>
 <h2 id="concatenate-vcf-files">Concatenate VCF files</h2>
@@ -1437,8 +1437,8 @@ <h2 id="concatenate-vcf-files">Concatenate VCF files</h2>
 </code></pre>
 <pre><code>## Checking the headers and starting positions of 2 files
 ## [W::bcf_hdr_merge] Trying to combine "MQ" tag definitions of different types
-## Concatenating eg/aln.bt.vcf.gz   0.019636 seconds
-## Concatenating eg/aln.hc.vcf.gz   0.022432 seconds
+## Concatenating eg/aln.bt.vcf.gz   0.017026 seconds
+## Concatenating eg/aln.hc.vcf.gz   0.023805 seconds
 ## 19997
 </code></pre>
 <p>Removing duplicates requires indexed VCF files; the <code>-f</code> parameter is
@@ -1484,7 +1484,7 @@ <h2 id="decomposing-and-normalising-variants">Decomposing and normalising varian
 <p>Convert MNV into SNVs.</p>
 <pre><code class="language-bash">bcftools norm -a eg/ex.vcf | tail -2
 </code></pre>
-<pre><code>## Lines   total/split/realigned/skipped:   6/0/0/0
+<pre><code>## Lines   total/split/joined/realigned/skipped:    6/0/0/0/0
 ## 1    25563113    .   C   G   .   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=2.621;DB;DP=20;FS=0;HRun=0;HaplotypeScore=101.749;MQ0=0;MQ=55.8;MQRankSum=-1.91;QD=11.05;ReadPosRankSum=0.4;set=variant   GT:AD:DP:GQ:PL  0/1:14,6:20:99:260,0,486    0/0:14,6:20:99:260,0,486    1/1:14,6:20:99:260,0,486
 ## 1    25563114    .   C   G   .   PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=2.621;DB;DP=20;FS=0;HRun=0;HaplotypeScore=101.749;MQ0=0;MQ=55.8;MQRankSum=-1.91;QD=11.05;ReadPosRankSum=0.4;set=variant   GT:AD:DP:GQ:PL  0/1:14,6:20:99:260,0,486    0/0:14,6:20:99:260,0,486    1/1:14,6:20:99:260,0,486
 </code></pre>
@@ -1609,5 +1609,5 @@ <h2 id="stargazers-over-time">Stargazers over time</h2>
 
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