[j6163m]

A searching of BAM files in Escritorio directory gives the next output:

ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~/Escritorio/picard-tools-1.128$ ls -lh /home/ubuntu/Escritorio/*.bam
-rw-rw-r-- 1 ubuntu ubuntu 83M may 16 19:20 /home/ubuntu/Escritorio/output.bam
-rw-rw-r-- 1 ubuntu ubuntu 0 may 17 21:28 /home/ubuntu/Escritorio/OUTPUT=output.bam
-rw-rw-r-- 1 ubuntu ubuntu 0 may 16 19:19 /home/ubuntu/Escritorio/test.bam

And showing the first 10 lines of output.bam:

ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~/Escritorio$ head -10 output.bam
�BC�U�?K1��Z[�"�����jɿ��
!>R�5ld�B�4��C��ZI�a��@\?�[�A�K�#���I~/�K���sas�k�������#r!�,9�
�\h�582
9嚹�O�&�D
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E�FF'�T*�"R211^�5eJ+7���>O�#s���/ez�#3��r"�wK��Hb$Aߍ��fs�'/D悏��-��l^��&��v׌��Qj��nT�+��aN�.�^#6�V��,cwu���,��p��8k����2b0<���ġ��Y�$`�x�Bx�����^������iK
������}��F/S��&N>�Ԥ��d���' �}���]�@�>>���^�֖�>GMw��^���Møη��(��o�d܎����޾���˿>���r�_������w�z��-��������}���h��0O�*���/C?��$N��̚<��m��e�~���qYTu]F��nӼ�|�u�U�&uZ�u��A��Q��6��6M�6Ip�M"���G�7�iZ��7o�m�6���m=i~0�ͻ��Y�F���=��<z�
�>�v���sߟ�~��I7��؏��[�����'k�p;Y��n���~�MV7Y
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W�G�l링Af���A�TAV۪�����e��[ْa����^��R�G���C�a៩�cz��:�����Ыrͮ&�{��\\�|�/�Y�1�n���܃�ɥ�h�Н�g�a8JG��k�h�,����_������s��t��R������AewrP�[<��ny~��'K^��D����IK4

Thatś right or wrong?

Waiting for your answer,please, thank you very much.

Juan M.

[GenoMax]

@Juan M: bam files are binary data so you can't read/view them directly (a text file command like 'head' will not work). That is the reason you only saw garbled data on screen (and your last post was tagged as spam since you pasted that data in). So what you have does look like a binary bam file.

I was hoping that @ulz_peter would chime in by now on a possible update to the manual.

[j6163m]

Thank you GenoMax.

Please, could you send me the new updated manual(or advise me to download it) when it was available?

Thankś again.

Juan M.

[sayali]

Thank a lot for the document.
I have a suggestion here. You can use cutadapt software after FastQC if the quality of the sequenced reads is not good.

[hafiztalha]

ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: IndelRealigner

having same error again and again. i have tried updating java , also i have latest GATK 3.7. can any one help me ?