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[]()&
**[]()&**
- - &
.[]()&.
### []()[]()&###
### []()&###
### **&###
1. style="text-align: left; float: none; ">Locate and modify&1. Locate and modify
2000](../uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")&
2](../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")&
2); its mate is mapped to 37 on the reverse strand (32). Read r002 has&
2. style="text-align: left; float: none; ">&2. Check Putty settings:
[](7D_Enhanced_hypercube.png)&
access&
access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is&
&
Analyzer](Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png "Intel Trace Analyzer")&
and comes to IT4I (represented by the blue dashed line). The data&
Anselm](../../anselm-cluster-documentation/Authorization_chain.png "Authorization chain")&
&
&
&
are mandatory, the rest is optional but strongly recommended. Each line&
class="anchor-link">&
class="Apple-converted-space">&
class="discreet visualHighlight">&
class="emphasis">&
class="glossaryItem">&
class="highlightedSearchTerm">&
class="highlightedSearchTerm">SSH</span><span>&highlightedSearchTerm
class="hps">&
class="hps">&
class="hps">More</span> <span class="hps">&
class="hps trans-target-highlight">&
class="internal-link">&
class="internal-link"><span id="result_box" class="short_text"><span&
class="monospace">&
class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE&LAPACKE modelu, which includes Intel's LAPACKE
class="n">&
### class="n">&###
class="n">&
class="pre">&
class="pun">node_group_key&
class="short_text"><span&
class="smarterwiki-popup-bubble-body"><span&
class="smarterwiki-popup-bubble-links-container"><span&
class="smarterwiki-popup-bubble-links-row">[{.smarterwiki-popup-bubble-link-favicon}](http://maps.google.com/maps?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google Maps"){.smarterwiki-popup-bubble-link}[{.smarterwiki-popup-bubble-link-favicon}](http://www.google.com/search?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google"){.smarterwiki-popup-bubble-link}[](http://www.google.com/search?hl=com&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span></span></span></span></span>&
class="smarterwiki-popup-bubble-links"><span&
class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped"><span&&
class="smarterwiki-popup-bubble-tip"></span><span
Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png/@@images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png "VPN Contacting Cluster")](../vpn_contacting_https_cluster.png)&
Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png "VPN Contacting Cluster")](../vpn_contacting_https.png)&
Cluster](https://docs.it4i.cz/salomon/vpn_contacting.png/@@images/9ccabccf-581a-476a-8c24-ce9842c3e657.png "VPN Contacting Cluster")](../vpn_contacting.png)&&
column and referenced from the genotype fields as 1-based indexes to&
component where they can be analysed directly by the user that produced&
connection](https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpeg "Successfull connection")](../../anselm-cluster-documentation/anyconnecticon.jpg)&
Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png "VPN Succesfull Connection")](../vpn_successfull_connection.png)&&
Connect](Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")&
contains a P (padding) operation which correctly aligns the inserted&
.contenttype-file}&
[](cygwin-and-x11-forwarding.html)&
data, the separator indicates whether the data are phased (|) or&
[{.image-inline width="451"&
deletion, replacement, and a large deletion. The REF columns shows the&
described by the annotation in the INFO column, the coordinate is that&
detection](../java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg "Java detection")&
disease definitions from the lists. Thus, virtual panels can be&
</div>&
<div>&
<div class="itemizedlist">&
<div id="d4841e18">&
<div id="d4841e21">&
<div id="d4841e24">&
<div id="d4841e27">&
<div id="d4841e30">&
<div id="d4841e34">&
<div id="d4841e37">&
&
file](../instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg "Installation file")&
filters available. The tool includes a genomic viewer (Genome Maps 30)&
&
[](Fluent_Licence_1.jpg)&
[](Fluent_Licence_2.jpg)&
[](Fluent_Licence_3.jpg)&
[](Fluent_Licence_4.jpg)&
for each sequenced patient. These lists files together with primary and&
forwarding style="text-align: left; float: none; ">&
genomic coordinates.](images/fig6.png.1 "fig6.png")&
genomic position or region. All alternate alleles are listed in the ALT&
[](gnome-compute-nodes-over-vnc.png)&
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### Gnome on Windows**&### Gnome on Windows
[](gnome-terminal.png)&
height="513"}](ddt1.png)&
[****](TightVNC_login.png)&
[](PuTTY_host_Salomon.png)&
[](PuTTY_open_Salomon.png)&
[](PuTTY_save_Salomon.png)&
[](totalview1.png)&
&
&
id="Key_management" class="mw-headline">Key management&
increases.](images/fig5.png.1 "fig5.png")&
insertion; the third a SNP; the fourth a large structural variant&
instalation](../successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg "Successfull instalation")&
](../copy_of_vpn_web_install_3.png)&
Install](https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png "VPN Install")](../vpn_web_download_2.png)&
Install](https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png "VPN Install")](../vpn_web_download.png)&
Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)[
Install](https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png "VPN Install")](../vpn_web_install_4.png)&
Install](https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png "VPN Install")](../vpn_web_login_2.png)&
Install](https://docs.it4i.cz/salomon/vpn_web_login.png/@@images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png "VPN Install")](../vpn_web_login.png)&
&
login](https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png "VPN login")](../vpn_login.png)&&
&
login](../successfullconnection.jpg "successful login")&
](../../anselm-cluster-documentation/anyconnectcontextmenu.jpg)&&
mismatches. Read r004 is aligned across an intron, indicated by the N&
### Notes **&### Notes
of reference sequences. Notably, r001 is the name of a read pair.&
of the base before the variant. (b–f ) Alignments and VCF&
of the body describes variants present in the sampled population at one&
&
out.](images/fig1.png "Fig 1")&
[Pageant (for Windows&
[](PageantV.png)&
&
position of the first aligned base. The CIGAR string for this alignment&
Preferences](gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)&
pre-processor converts raw data into a list of variants and annotations&
present in the sequence field. The NM tag gives the number of&
profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")&
PuTTY - class="Apple-converted-space"> before we start SSH connection ssh-connection style="text-align: start; "}&
[](PuttyKeygenerator_001V.png)&
[](PuttyKeygenerator_002V.png)&
[](20150312_143443.png)&
[](PuttyKeygenerator_004V.png)&
[](PuttyKeygenerator_005V.png)&
[](PuttyKeygenerator_006V.png)&
[](PuttyKeygeneratorV.png)&
[](PuTTY_keyV.png)&
reference bases replaced by the haplotype in the ALT column. The&
&
&
&
&
&
&
representations of different sequence variants: SNP, insertion,&
&
Rstudio&Rstudio**
&
[](../salomon-2)&
[](salomon)&
[](salomon)&
&
&
&![]](salomon-3.jpeg)
&
](gdmdisablescreensaver.png)&
[](vtune-amplifier)&
Screenshot](Snmekobrazovky20141204v12.56.36.png "CUBE Screenshot")&
&
secondary (alignment) data files are stored in IT4I sequence DB and&
sequences. Padding operations can be absent when an aligner does not&
session](../../../../salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png "Default Gnome session")](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)&
shows an example of a deletion (present in SAMPLE1) and a replacement of&
<span&
<span&
[<span class="anchor-link">&
<span class="discreet">&
<span class="discreet"></span>&
<span class="glossaryItem">&
<span class="glossaryItem">&
<span class="hps">&
<span class="hps alt-edited">&
<span class="listitem">&
<span class="s1">&
<span class="WYSIWYG_LINK">&
<span dir="auto">&
<span id="__caret">&
<span id="__caret"><span id="__caret"></span></span>&
(<span id="result_box">&
<span id="result_box" class="short_text"><span class="hps">&
<span id="result_box"><span class="hps">&
</span></span>&
</span> <span&
<span><span>&
</span> <span class="hps">&
</span> <span class="hps">&
</span> <span class="hps">who have a valid</span> <span&
<span><span class="monospace">&
<span><span>Introduction&###Introduction
</span></span><span><span>&
</span></span></span></span><span><span>&
</span></span><span><span><span><span>&
.<span style="text-align: left; "> </span>&
<span style="text-align: start; ">&
{.state-missing-value
style="text-align: left; float: none; ">&
style="text-align: left; float: none; ">&
style="text-align: left; float: none; ">change it&change it to
style="text-align: left; float: none; ">Check Putty settings:&
style="text-align: left; float: none; ">Enable X11&Enable X11
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style="text-align: left; float: none; "> &
style="text-align: start; ">&
style="text-align: start; float: none; ">&
&
**Summary&**Summary**
support multiple sequence alignment. The last six bases of read r003 map&
Tape Library T950B**&**Tape Library T950B**
.text}.&
.text}&
that enables the representation of the variants in the corresponding&
]&![]
to position 9, and the first five to position 29 on the reverse strand.&
to</span>&
[](totalview2.png)&
tunnel](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png "PuTTY Tunnel")](putty-tunnel.png)&
two bases by another base (SAMPLE2); the second line shows a SNP and an&
unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in&
uploaded to the discovery (candidate priorization) or diagnostic&
users)](putty/PageantV.png)&
use simplest representation possible and lowest coordinate in cases&
&
&
vncviewer](../../../../anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png "Vncviewer")&
[&
Workflow](virtualization-job-workflow "Virtualization Job Workflow")&
&
[]() &
&
[**](TightVNC_login.png)&
[](gnome-terminal.png)&
[](gnome-compute-nodes-over-vnc.png)&
screensaver](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&